Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

comparison add_expression_HPA.R @ 10:07858c6dbbff draft

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"planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
author proteore
date Wed, 22 Jan 2020 15:26:11 +0000
parents 28d51adf8292
children f8d3a8a2f2e5
comparison
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9:28d51adf8292 10:07858c6dbbff
1 # Read file and return file content as data.frame 1 # Read file and return file content as data.frame
2 read_file <- function(path,header){ 2 read_file <- function(path,header){
3 file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE) 3 file <- read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F)
4 if (inherits(file,"try-error")){ 4 return(file)
5 stop("File not found !")
6 }else{
7 return(file)
8 }
9 } 5 }
10 6
11 #convert a string to boolean 7 #convert a string to boolean
12 str2bool <- function(x){ 8 str2bool <- function(x){
13 if (any(is.element(c("t","true"),tolower(x)))){ 9 if (any(is.element(c("t","true"),tolower(x)))){
173 ids = ids[which(!is.na(ids))] 169 ids = ids[which(!is.na(ids))]
174 } 170 }
175 check_ensembl_geneids(ids) 171 check_ensembl_geneids(ids)
176 172
177 # Read protein atlas 173 # Read protein atlas
178 protein_atlas = args$atlas 174 protein_atlas = read_file(args$atlas, T)
179 protein_atlas = read_file(protein_atlas, T)
180 175
181 # Add expression 176 # Add expression
182 output = args$output 177 output = args$output
183 options = strsplit(args$select, ",")[[1]] 178 options = strsplit(args$select, ",")[[1]]
184 res = add_expression(ids, protein_atlas, options) 179 res = add_expression(ids, protein_atlas, options)