maxquant_phosphopeptide_intensity: MaxQuantProcessingScript.R annotate

annotate MaxQuantProcessingScript.R @ 0:b09ed1684301 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15"

author	galaxyp
date	Thu, 04 Nov 2021 18:35:10 +0000
parents
children

rev	line source
0 b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	1 #!/usr/bin/env Rscript
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	2 # libraries
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	3 library(optparse)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	4 library(data.table)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	5 library(stringr)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	6 #library(ggplot2)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	7 #library(PTXQC)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	8 #require(PTXQC)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	9 #require(methods)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	10
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	11 # title: "MaxQuant Processing Script"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	12 # author: "Larry Cheng"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	13 # date: "February 19, 2018"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	14 #
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	15 # # MaxQuant Processing Script
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	16 # Takes MaxQuant Phospho (STY)sites.txt file as input and performs the following (in order):
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	17 # 1) Runs the Proteomics Quality Control software
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	18 # 2) Remove contaminant and reverse sequence rows
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	19 # 3) Filters rows based on localization probability
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	20 # 4) Extract the quantitative data
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	21 # 5) Sequences phosphopeptides
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	22 # 6) Merges multiply phosphorylated peptides
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	23 # 7) Filters out phosphopeptides based on enrichment
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	24 # The output file contains the phosphopeptide (first column) and the quantitative values for each sample
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	25 #
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	26 # ## Revision History
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	27 # Rev. 2018-02-19 :break up analysis script into "MaxQuant Processing Script" and "Phosphopeptide Processing Script"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	28 # Rev. 2017-12-12 :added PTXQC
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	29 # added additional plots and table outputs for quality control
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	30 # allowed for more than 2 samples to be grouped together (up to 26 (eg, 1A, 1B, 1C, etc))regexSampleNames <-
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	31 # "\\.(\\d+)[A-Z]$"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	32 # converted from .r to .rmd file to knit report for quality control
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	33 # Rev. 2016-09-11 :automated the FDR cutoffs; removed the option to data impute multiple times
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	34 # Rev. 2016-09-09 :added filter to eliminate contaminant and reverse sequence rows
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	35 # Rev. 2016-09-01 :moved the collapse step from after ANOVA filter to prior to preANOVA file output
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	36 # Rev. 2016-08-22 :changed regexpression to regexSampleNames <- "\\.(\\d+)[AB]$" so that it looks at the end of string
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	37 # Rev. 2016-08-05 :Removed vestigial line (ppeptides <- ....)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	38 # Rev. 2016-07-03 :Removed row names from the write.table() output for ANOVA and PreANOVA
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	39 # Rev. 2016-06-25 :Set default Localization Probability cutoff to 0.75
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	40 # Rev. 2016-06-23 :fixed a bug in filtering for pY enrichment by resetting the row numbers afterwards
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	41 # Rev. 2016-06-21 :test18 + standardized the regexpression in protocol
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	42
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	43 ## Variables to change for each input file
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	44 ## ```{r}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	45 ## #Location of MaxQuant txt folder
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	46 ## # C:\Users\art\src\ppenrich\postMQanalysis\step2.1
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	47 ## dir_txtfolder <- "C:/Users/art/src/ppenrich/postMQanalysis/step2.1"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	48 ## #Input Filename
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	49 ## inputFilename <- paste0(dir"/Phospho (STY)Sites.txt"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	50 ## #Column number for the Intensity of the first sample
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	51 ## startCol <- 58
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	52 ## #Number of runs
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	53 ## numSamples <- 6
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	54 ## #Column number of "Number.of.Phospho..STY."
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	55 ## phosphoCol <- 37
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	56 ## #pY or pST enriched samples (ie, "Y" or "ST")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	57 ## enriched <- "ST"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	58 ## #output filename
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	59 ## outputfilename = "outputfile_STEP2.txt"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	60 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	61 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	62 ## ## Other modifiable variables
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	63 ## ```{r}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	64 ## #Column interval between the Intensities of samples (eg, 1 if subsequent column; 2 if every other column)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	65 ## intervalCol <- 1
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	66 ## #Localization Probability Cutoff
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	67 ## localProbCutoff <- 0.75
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	68 ## #merge identical phosphopeptides by ("sum" or "average") the intensities
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	69 ## collapse_FUN = "sum"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	70 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	71
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	72 # parse options
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	73 option_list <- list(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	74 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	75 c("-i", "--input"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	76 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	77 default = NA,
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	78 type = "character",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	79 help = "A MaxQuant Phospho (STY)Sites.txt"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	80 ),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	81 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	82 c("-o", "--output"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	83 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	84 default = "output.tsv",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	85 type = "character",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	86 help = "output file"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	87 ),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	88 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	89 c("-e", "--enriched"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	90 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	91 default = "output.tsv",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	92 type = "character",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	93 help = "pY or pST enriched samples (ie, 'Y' or 'ST')"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	94 ),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	95 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	96 c("-n", "--numSamples"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	97 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	98 default = 3,
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	99 type = "integer",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	100 help = "Number of samples"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	101 ),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	102 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	103 c("-p", "--phosphoCol"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	104 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	105 default = 13,
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	106 type = "integer",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	107 help = "Column number of Number.of.Phospho..STY."
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	108 ),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	109 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	110 c("-s", "--startCol"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	111 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	112 default = 24,
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	113 type = "integer",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	114 help = "Column number for the Intensity of the first sample"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	115 ),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	116 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	117 c("-I", "--intervalCol"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	118 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	119 default = 1,
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	120 type = "integer",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	121 help = "Column interval between the Intensities of samples (eg, 1 if subsequent column; 2 if every other column"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	122 ),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	123 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	124 c("-l", "--localProbCutoff"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	125 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	126 default = 0.75,
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	127 type = "double",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	128 help = "Localization Probability Cutoff"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	129 ),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	130 make_option(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	131 c("-f", "--collapse_func"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	132 action = "store",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	133 default = "sum",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	134 type = "character",
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	135 help = "merge identical phosphopeptides by ('sum' or 'average') the intensities"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	136 )
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	137 )
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	138 args <- parse_args(OptionParser(option_list=option_list))
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	139 # Check parameter values
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	140
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	141 if (! file.exists(args$input)) {
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	142 stop((paste("File", args$input, "does not exist")))
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	143 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	144 inputFilename <- args$input
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	145 outputfilename <- args$output
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	146 localProbCutoff <- args$localProbCutoff
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	147 numSamples <- args$numSamples
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	148 phosphoCol <- args$phosphoCol
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	149 startCol <- args$startCol
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	150 intervalCol <- args$intervalCol
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	151 enriched <- "ST"
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	152 collapse_FUN = args$collapse_func
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	153
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	154 ### FUNCTIONS
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	155
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	156 #function to generate phosphopeptide and build list when applied
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	157 phosphopeptide_func <- function(df) {
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	158
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	159 #generate peptide sequence and list of phosphopositions
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	160 phosphoprobsequence <- strsplit(as.character(df["Phospho (STY) Score diffs"]), "")[[1]]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	161 output <- vector()
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	162 phosphopeptide <- ""
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	163 counter <- 0 #keep track of position in peptide
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	164 phosphopositions <- vector() #keep track of phosphorylation positions in peptide
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	165 score_diff <- ""
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	166 for (chara in phosphoprobsequence){
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	167 #build peptide sequence
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	168 if (!(chara == " " \| chara == "(" \| chara == ")" \| chara =="." \| chara =="-" \| chara == "0" \| chara == "1" \| chara == "2" \| chara == "3" \| chara =="4" \| chara == "5" \| chara == "6" \| chara == "7" \| chara =="8" \| chara =="9")) {
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	169 phosphopeptide <- paste(phosphopeptide,chara,sep="")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	170 counter <- counter + 1
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	171 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	172 #generate score_diff
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	173 if (chara == "-" \| chara =="." \| chara == "0" \| chara == "1" \| chara == "2" \| chara == "3" \| chara =="4" \| chara == "5" \| chara == "6" \| chara == "7" \| chara =="8" \| chara =="9"){
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	174 score_diff <- paste(score_diff,chara,sep="")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	175 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	176 #evaluate score_diff
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	177 if (chara == ")" ){
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	178 score_diff <- as.numeric(score_diff)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	179 #only consider a phosphoresidue if score_diff > 0
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	180 if (score_diff > 0) {
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	181 phosphopositions <- append(phosphopositions, counter)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	182 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	183 score_diff <- ""
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	184 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	185 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	186
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	187 #generate phosphopeptide sequence (ie, peptide sequence with "p"'s)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	188 counter <- 1
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	189 phosphoposition_correction1 <- -1 #used to correct phosphosposition as "p"'s are inserted into the phosphopeptide string
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	190 phosphoposition_correction2 <- 0 #used to correct phosphosposition as "p"'s are inserted into the phosphopeptide string
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	191 while (counter <= length(phosphopositions) ) {
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	192 phosphopeptide <- paste(substr(phosphopeptide,0,phosphopositions[counter]+phosphoposition_correction1),"p",substr(phosphopeptide,phosphopositions[counter]+phosphoposition_correction2,nchar(phosphopeptide)),sep="")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	193 counter <- counter + 1
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	194 phosphoposition_correction1 <- phosphoposition_correction1 + 1
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	195 phosphoposition_correction2 <- phosphoposition_correction2 + 1
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	196 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	197
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	198 #building phosphopeptide list
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	199 output <- append(output,phosphopeptide)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	200 return(output)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	201 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	202 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	203 ## ## Run Proteomics Quality Control for MaxQuant Results
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	204 ## (Bielow C et al. J Proteome Res. 2016 PMID: 26653327)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	205 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	206 ## ```{r echo=FALSE}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	207 ## library(PTXQC)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	208 ## require(PTXQC)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	209 ## require(methods)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	210 ## txt_folder <- dir_txtfolder
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	211 ## r = createReport(txt_folder)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	212 ## cat(paste0("\nReport has been generated inside the MaxQuant txt folder '", r$report_file, "'\n\n"))
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	213 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	214 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	215 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	216 ## Perform filters on contaminants, reverse sequences, and localization probability
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	217
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	218 fullData <- read.table(file = inputFilename, sep ="\t", header=T, quote="")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	219
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	220 #Filter out contaminant rows and reverse rows
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	221 filteredData <- subset(fullData,!grepl("CON__", Proteins))
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	222 filteredData <- subset(filteredData,!grepl("_MYCOPLASMA", Proteins))
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	223 filteredData <- subset(filteredData,!grepl("CONTAMINANT_", Proteins))
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	224 filteredData <- subset(filteredData,!grepl("REV__", Protein)) #since REV__ rows are blank in the first column (Proteins)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	225 write.table(filteredData, file = "filteredData.txt", sep = "\t", col.names=TRUE, row.names=FALSE)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	226
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	227 #Data filtered by localization probability
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	228 locProbFilteredData <- filteredData[filteredData$Localization.prob>=localProbCutoff,]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	229
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	230 ## Localization probability
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	231 ## #visualize locprob cutoff
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	232 locProbGraphData <- data.frame(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	233 group = c(paste(">",toString(localProbCutoff),sep=""), paste("<",toString(localProbCutoff),sep="")),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	234 value = c(nrow(locProbFilteredData)/nrow(filteredData)100, (nrow(filteredData)-nrow(locProbFilteredData))/nrow(filteredData)100)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	235 )
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	236 ## library(ggplot2)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	237 ## locProbGraph <- ggplot(locProbGraphData, aes(x="", y=value, fill=group)) +
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	238 ## geom_bar(width = 0.5, stat = "identity", color="black")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	239 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	240 ## locProbGraph
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	241
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	242 ## Extract out quantitative values
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	243 #Extract out quantitative values
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	244 quantData <- locProbFilteredData[,seq(from=startCol, by=intervalCol, length.out=numSamples)]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	245 write.table(quantData, file = "quantdata.txt", sep = "\t", col.names=TRUE, row.names=FALSE)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	246 #head(quantData)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	247 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	248 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	249 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	250 ## ## Generate Phosphopeptide Sequence
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	251 ## First few rows of the phosphopeptide column:
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	252 #for latest version of MaxQuant (Version 1.5.3.30)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	253 dataTable <- data.frame(locProbFilteredData[,1:8],locProbFilteredData[,phosphoCol],locProbFilteredData[,phosphoCol+1],locProbFilteredData[,phosphoCol+2],locProbFilteredData[,phosphoCol+3],locProbFilteredData[,phosphoCol+4],locProbFilteredData[,phosphoCol+5],locProbFilteredData[,phosphoCol+6],locProbFilteredData[,phosphoCol+7],quantData)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	254 colnames(dataTable) <- c("Proteins","Positions within proteins", "Leading proteins", "Protein", "Protein names", "Gene names", "Fasta headers", "Localization prob", "Number of Phospho (STY)", "Amino Acid", "Sequence window","Modification window", "Peptide window coverage", "Phospho (STY) Probabilities", "Phospho (STY) Score diffs", "Position in peptide", colnames(quantData))
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	255 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	256 #Generate column in dataTable for the predicted phosphopeptide
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	257 dataTable$Phosphopeptide <- apply(dataTable,1,phosphopeptide_func)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	258 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	259 #Move Quant columns to the end
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	260 movetolast <- function(data, move) { #moves columns to the end of dataframe
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	261 data[c(setdiff(names(data), move), move)]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	262 }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	263 dataTable <- movetolast(dataTable,c(colnames(quantData)))
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	264 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	265 #Make new data frame containing only Phosphopeptides to be mapped to quant data (merge_df)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	266 dataTable <- setDT(dataTable, keep.rownames=TRUE) #row name will be used to map
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	267 merge_df <- data.frame(as.integer(dataTable$rn), dataTable$Phosphopeptide) #row index to merge data frames
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	268 colnames(merge_df) <- c("rn", "Phosphopeptide")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	269 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	270 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	271 head(merge_df)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	272 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	273 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	274 ## First few rows of the MaxQuant phosphoresidue score differences: Sequence representation for each of the possible PTM positions in each possible configuration, the difference is calculated between the identification score with the PTM added to that position and the best scoring identification where no PTM is added to that position. When this value is negative, it is unlikely that the particular modification is located at this position.
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	275 ## ```{r echo=FALSE}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	276 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	277 ## head(locProbFilteredData$Phospho..STY..Score.diffs)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	278 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	279 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	280 ## First few rows of data with Phosphopeptide Sequence.
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	281 ## ```{r echo=FALSE }
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	282 ## # Add Phosphopeptide column to quant columns for quality control checking
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	283 quantData_qc <- as.data.frame(quantData)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	284 setDT(quantData_qc, keep.rownames=TRUE) #will use to match rowname to data
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	285 quantData_qc$rn <- as.integer(quantData_qc$rn)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	286 quantData_qc <- merge(merge_df,quantData_qc, by="rn")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	287 quantData_qc$rn <- NULL #remove rn column
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	288 head(quantData_qc)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	289 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	290 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	291 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	292 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	293 ## ## Collapse multiphosphorylated peptides
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	294 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	295 ## Before collapse:
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	296 ## ```{r echo=FALSE}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	297 ## summary(quantData_qc)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	298 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	299 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	300 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	301 ## After collapse:
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	302 ## ```{r echo=FALSE}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	303 #Collapse multiphosphorylated peptides
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	304 quantData_qc_collapsed <- data.table(quantData_qc, key = "Phosphopeptide")
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	305 quantData_qc_collapsed <- aggregate(. ~ Phosphopeptide,quantData_qc, FUN= collapse_FUN)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	306 summary(quantData_qc_collapsed)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	307 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	308 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	309 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	310 ## % of phosphopeptides that are multiphosphorylated is roughly ~
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	311 ## ```{r echo=FALSE}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	312 (nrow(quantData_qc) - nrow(quantData_qc_collapsed))/nrow(quantData_qc)/2
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	313 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	314 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	315 ## Breakdown of pY, pS, and pT before enrichment filter
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	316 ## ```{r echo=FALSE}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	317 ## library(stringr)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	318 pY_data <- quantData_qc_collapsed[str_detect(quantData_qc_collapsed$Phosphopeptide, "pY"),]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	319 pS_data <- quantData_qc_collapsed[str_detect(quantData_qc_collapsed$Phosphopeptide, "pS"),]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	320 pT_data <- quantData_qc_collapsed[str_detect(quantData_qc_collapsed$Phosphopeptide, "pT"),]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	321 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	322 pY_num <- nrow(pY_data)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	323 pS_num <- nrow(pS_data)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	324 pT_num <- nrow(pT_data)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	325 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	326 ## #visualize enrichment
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	327 enrichGraphData <- data.frame(
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	328 group = c("pY", "pS", "pT"),
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	329 value = c(pY_num, pS_num, pT_num)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	330 )
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	331 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	332 ## library(ggplot2)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	333 ## enrichGraph <- ggplot(enrichGraphData, aes(x="", y=value, fill=group)) +
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	334 ## geom_bar(width = 0.5, stat = "identity", color="black") + coord_polar("y", start=0)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	335 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	336 ## enrichGraph
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	337 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	338 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	339 ## ## Filter phosphopeptides by enrichment
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	340 ## ```{r echo=FALSE}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	341 ## #Data filtered by enrichment
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	342 ## library(stringr)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	343 if (enriched == "Y"){
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	344 quantData_qc_enrichment <- quantData_qc_collapsed[str_detect(quantData_qc_collapsed$Phosphopeptide, "pY"),]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	345 } else if ( enriched == "ST" ) {
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	346 quantData_qc_enrichment <- quantData_qc_collapsed[str_detect(quantData_qc_collapsed$Phosphopeptide, "pS") \| str_detect(quantData_qc_collapsed$Phosphopeptide, "pT"),]
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	347 } else { print("Error in enriched variable. Set to either 'Y' or 'ST'")}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	348 ## ```
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	349 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	350 ##
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	351 ## ```{r echo=FALSE}
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	352 ## #output files
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	353 ## #write.table(quantData_qc, file="BeforeCollapse.txt", sep="\t", row.names = FALSE) #for quality control
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	354 ## #write.table(quantData_qc_collapsed, file="AfterCollapse.txt", sep="\t", row.names = FALSE) #for quality control
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	355 write.table(quantData_qc_enrichment, file=outputfilename, sep="\t", quote = FALSE, row.names = FALSE)
b09ed1684301 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15" galaxyp parents: diff changeset	356 ## ```

Mercurial > repos > galaxyp > maxquant_phosphopeptide_intensity

annotate MaxQuantProcessingScript.R @ 0:b09ed1684301 draft default tip