Mercurial > repos > computational-metabolomics > mspurity_frag4feature

comparison filterFragSpectra.R @ 8:cb4aeec93d49 draft

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 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author computational-metabolomics
date Wed, 12 Jun 2024 16:08:23 +0000
parents e9fbb65451f6
children
comparison
equal deleted inserted replaced
7:e9fbb65451f6 8:cb4aeec93d49
7 option_list <- list( 7 option_list <- list(
8 make_option("--out_rdata", type = "character"), 8 make_option("--out_rdata", type = "character"),
9 make_option("--out_peaklist_prec", type = "character"), 9 make_option("--out_peaklist_prec", type = "character"),
10 make_option("--out_peaklist_frag", type = "character"), 10 make_option("--out_peaklist_frag", type = "character"),
11 make_option("--pa", type = "character"), 11 make_option("--pa", type = "character"),
12
13 make_option("--ilim", default = 0.0), 12 make_option("--ilim", default = 0.0),
14 make_option("--plim", default = 0.0), 13 make_option("--plim", default = 0.0),
15
16 make_option("--ra", default = 0.0), 14 make_option("--ra", default = 0.0),
17 make_option("--snr", default = 0.0), 15 make_option("--snr", default = 0.0),
18
19 make_option("--rmp", action = "store_true"), 16 make_option("--rmp", action = "store_true"),
20 make_option("--snmeth", default = "median", type = "character"), 17 make_option("--snmeth", default = "median", type = "character"),
21 make_option("--allfrag", action = "store_true") 18 make_option("--allfrag", action = "store_true")
22 ) 19 )
23 20
24 opt <- parse_args(OptionParser(option_list = option_list)) 21 opt <- parse_args(OptionParser(option_list = option_list))
25 print(opt) 22 print(opt)
26 23
27 24
28 loadRData <- function(rdata_path, name) { 25 loadRData <- function(rdata_path, name) {
29 #loads an RData file, and returns the named xset object if it is there 26 # loads an RData file, and returns the named xset object if it is there
30 load(rdata_path) 27 load(rdata_path)
31 return(get(ls()[ls() %in% name])) 28 return(get(ls()[ls() %in% name]))
32 } 29 }
33 30
34 # Requires 31 # Requires
35 pa <- loadRData(opt$pa, "pa") 32 pa <- loadRData(opt$pa, "pa")
36 33
37 if (is.null(opt$rmp)) { 34 if (is.null(opt$rmp)) {
38 opt$rmp <- FALSE 35 opt$rmp <- FALSE
39 }else{ 36 } else {
40 opt$rmp <- TRUE 37 opt$rmp <- TRUE
41 } 38 }
42 39
43 if (is.null(opt$allfrag)) { 40 if (is.null(opt$allfrag)) {
44 opt$allfrag <- FALSE 41 opt$allfrag <- FALSE
45 }else{ 42 } else {
46 opt$allfrag <- TRUE 43 opt$allfrag <- TRUE
47 } 44 }
48 45
49 pa <- filterFragSpectra(pa, 46 pa <- filterFragSpectra(pa,
50 ilim = opt$ilim, 47 ilim = opt$ilim,
51 plim = opt$plim, 48 plim = opt$plim,
52 ra = opt$ra, 49 ra = opt$ra,
53 snr = opt$snr, 50 snr = opt$snr,
54 rmp = opt$rmp, 51 rmp = opt$rmp,
55 allfrag = opt$allfrag, 52 allfrag = opt$allfrag,
56 snmeth = opt$snmeth) 53 snmeth = opt$snmeth
54 )
57 55
58 print(pa) 56 print(pa)
59 save(pa, file = opt$out_rdata) 57 save(pa, file = opt$out_rdata)
60 58
61 # get the msms data for grpid from the purityA object 59 # get the msms data for grpid from the purityA object
80 } 78 }
81 79
82 80
83 81
84 if (length(pa) > 0) { 82 if (length(pa) > 0) {
85
86 if (length(pa@grped_ms2) == 0) { 83 if (length(pa@grped_ms2) == 0) {
87 message("No spectra available") 84 message("No spectra available")
88 } else { 85 } else {
89
90 # get group ids 86 # get group ids
91 grpids <- unique(as.character(pa@grped_df$grpid)) 87 grpids <- unique(as.character(pa@grped_df$grpid))
92 88
93 # loop through all the group ids 89 # loop through all the group ids
94 df_fragments <- plyr::adply(grpids, 1, msmsgrp, pa = pa) 90 df_fragments <- plyr::adply(grpids, 1, msmsgrp, pa = pa)
95 df_fragments <- merge(df_fragments, pa@puritydf[, c("pid", "acquisitionNum", "precursorScanNum")], by = "pid") 91 df_fragments <- merge(df_fragments, pa@puritydf[, c("pid", "acquisitionNum", "precursorScanNum")], by = "pid")
96 df_fragments <- df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz), ] 92 df_fragments <- df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz), ]
97 #select and reorder columns 93 # select and reorder columns
98 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")] 94 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")]
99 95
100 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)]) 96 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
101 97
102 print(head(pa@grped_df)) 98 print(head(pa@grped_df))