Mercurial > repos > computational-metabolomics > mspurity_combineannotations

comparison filterFragSpectra.R @ 0:de93f6aac760 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:21:39 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:de93f6aac760
1 library(optparse)
2 library(msPurity)
3 library(xcms)
4 print(sessionInfo())
5
6
7 option_list <- list(
8 make_option("--out_rdata", type = "character"),
9 make_option("--out_peaklist_prec", type = "character"),
10 make_option("--out_peaklist_frag", type = "character"),
11 make_option("--pa", type = "character"),
12
13 make_option("--ilim", default = 0.0),
14 make_option("--plim", default = 0.0),
15
16 make_option("--ra", default = 0.0),
17 make_option("--snr", default = 0.0),
18
19 make_option("--rmp", action = "store_true"),
20 make_option("--snmeth", default = "median", type = "character")
21 )
22
23 opt <- parse_args(OptionParser(option_list = option_list))
24 print(opt)
25
26
27 loadRData <- function(rdata_path, name) {
28 #loads an RData file, and returns the named xset object if it is there
29 load(rdata_path)
30 return(get(ls()[ls() %in% name]))
31 }
32
33 # Requires
34 pa <- loadRData(opt$pa, "pa")
35
36 if (is.null(opt$rmp)) {
37 opt$rmp <- FALSE
38 }else{
39 opt$rmp <- TRUE
40 }
41
42 pa <- filterFragSpectra(pa,
43 ilim = opt$ilim,
44 plim = opt$plim,
45 ra = opt$ra,
46 snr = opt$snr,
47 rmp = opt$rmp,
48 snmeth = opt$snmeth)
49
50 print(pa)
51 save(pa, file = opt$out_rdata)
52
53 # get the msms data for grpid from the purityA object
54 msmsgrp <- function(grpid, pa) {
55 msms <- pa@grped_ms2[grpid]
56
57 grpinfo <- pa@grped_df[pa@grped_df$grpid == grpid, ]
58
59 grpinfo$subsetid <- seq_len(nrow(grpinfo))
60 result <- plyr::ddply(grpinfo, ~subsetid, setid, msms = msms)
61 return(result)
62 }
63
64 # Set the relevant details
65 setid <- function(grpinfo_i, msms) {
66 msms_i <- msms[[1]][[grpinfo_i$subsetid]]
67 n <- nrow(msms_i)
68 msms_i <- data.frame(msms_i)
69 colnames(msms_i)[1:2] <- c("mz", "i")
70 m <- cbind("grpid" = rep(grpinfo_i$grpid, n), "pid" = rep(grpinfo_i$pid, n), "fileid" = rep(grpinfo_i$fileid, n), msms_i)
71 return(m)
72 }
73
74
75
76 if (length(pa) > 0) {
77
78 if (length(pa@grped_ms2) == 0) {
79 message("No spectra available")
80 } else {
81
82 # get group ids
83 grpids <- unique(as.character(pa@grped_df$grpid))
84
85 # loop through all the group ids
86 df_fragments <- plyr::adply(grpids, 1, msmsgrp, pa = pa)
87 df_fragments <- merge(df_fragments, pa@puritydf[, c("pid", "acquisitionNum", "precursorScanNum")], by = "pid")
88 df_fragments <- df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz), ]
89 #select and reorder columns
90 df_fragments <- df_fragments[, c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")]
91
92 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
93
94 print(head(pa@grped_df))
95 write.table(pa@grped_df, opt$out_peaklist_prec, row.names = FALSE, sep = "\t")
96 print(head(df_fragments))
97 write.table(df_fragments, opt$out_peaklist_frag, row.names = FALSE, sep = "\t")
98 }
99 }