Mercurial > repos > computational-metabolomics > mspurity_flagremove

annotate averageFragSpectra.R @ 0:353d48ece635 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 12:17:52 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
1 library(optparse)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
2 library(msPurity)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
3 library(xcms)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
4 print(sessionInfo())
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
5
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
6
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
7 get_av_spectra <- function(x) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
8
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
9 if (length(x$av_intra) > 0) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
10 av_intra_df <- plyr::ldply(x$av_intra)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
11
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
12 if (nrow(av_intra_df) == 0) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
13 av_intra_df <- NULL
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
14 }else{
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
15 av_intra_df$method <- "intra"
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
16 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
17
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
18 }else{
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
19 av_intra_df <- NULL
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
20 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
21
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
22 if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
23 av_inter_df <- NULL
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
24 }else{
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
25 av_inter_df <- x$av_inter
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
26 av_inter_df$method <- "inter"
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
27 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
28
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
29 if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
30 av_all_df <- NULL
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
31 }else{
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
32 av_all_df <- x$av_all
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
33 av_all_df$method <- "all"
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
34 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
35
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
36 combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
37
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
38 return(combined)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
39 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
40
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
41
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
42 option_list <- list(
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
43 make_option("--out_rdata", type = "character"),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
44 make_option("--out_peaklist", type = "character"),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
45 make_option("--pa", type = "character"),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
46 make_option("--av_level", type = "character"),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
47 make_option("--minfrac", default = 0.5),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
48 make_option("--minnum", default = 1),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
49 make_option("--ppm", default = 5.0),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
50 make_option("--snr", default = 0),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
51 make_option("--ra", default = 0),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
52 make_option("--av", default = "median", type = "character"),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
53 make_option("--sumi", action = "store_true"),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
54 make_option("--rmp", action = "store_true"),
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
55 make_option("--cores", default = 1)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
56 )
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
57
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
58 opt <- parse_args(OptionParser(option_list = option_list))
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
59 print(opt)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
60
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
61
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
62 load_r_data <- function(rdata_path, name) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
63 #loads an RData file, and returns the named xset object if it is there
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
64 load(rdata_path)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
65 return(get(ls()[ls() %in% name]))
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
66 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
67
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
68 # Requires
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
69 pa <- load_r_data(opt$pa, "pa")
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
70
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
71 pa@cores <- opt$cores
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
72
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
73 if (is.null(opt$rmp)) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
74 rmp <- FALSE
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
75 }else{
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
76 rmp <- TRUE
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
77 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
78
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
79 if (is.null(opt$sumi)) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
80 sumi <- FALSE
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
81 }else{
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
82 sumi <- TRUE
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
83 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
84
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
85 if (opt$av_level == "intra") {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
86 pa <- msPurity::averageIntraFragSpectra(pa,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
87 minfrac = opt$minfrac,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
88 minnum = opt$minnum,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
89 ppm = opt$ppm,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
90 snr = opt$snr,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
91 ra = opt$ra,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
92 av = opt$av,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
93 sumi = sumi,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
94 rmp = rmp,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
95 cores = opt$cores)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
96
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
97 } else if (opt$av_level == "inter") {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
98
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
99 pa <- msPurity::averageInterFragSpectra(pa,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
100 minfrac = opt$minfrac,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
101 minnum = opt$minnum,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
102 ppm = opt$ppm,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
103 snr = opt$snr,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
104 ra = opt$ra,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
105 av = opt$av,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
106 sumi = sumi,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
107 rmp = rmp,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
108 cores = opt$cores)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
109 } else if (opt$av_level == "all") {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
110
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
111 pa <- msPurity::averageAllFragSpectra(pa,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
112 minfrac = opt$minfrac,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
113 minnum = opt$minnum,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
114 ppm = opt$ppm,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
115 snr = opt$snr,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
116 ra = opt$ra,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
117 av = opt$av,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
118 sumi = sumi,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
119 rmp = rmp,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
120 cores = opt$cores)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
121 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
122
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
123 print(pa)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
124 save(pa, file = opt$out_rdata)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
125
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
126 if (length(pa) > 0) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
127
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
128 av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
129
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
130 if (nrow(av_spectra) == 0) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
131 message("No average spectra available")
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
132 } else {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
133 colnames(av_spectra)[1] <- "grpid"
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
134 av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid]
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
135
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
136 if ((length(pa@av_intra_params) > 0) || (length(pa@av_inter_params) > 0)) {
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
137 # Add some extra info (only required if av_intra or av_inter performed)
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
138 colnames(av_spectra)[2] <- "fileid"
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
139 av_spectra$avid <- seq_len(nrow(av_spectra))
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
140
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
141 filenames <- sapply(av_spectra$fileid,
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
142 function(x) names(pa@fileList)[as.integer(x)])
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
143 # filenames_galaxy <- sapply(
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
144 # av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
145
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
146 av_spectra <- as.data.frame(
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
147 append(av_spectra, list(filename = filenames), after = 2))
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
148 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
149
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
150
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
151 print(head(av_spectra))
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
152 write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t")
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
153
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
154 }
353d48ece635 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
155 }