Mercurial > repos > tomnl > track_rt_raw

annotate anticipated_purity_dims.R @ 7:ef046d5e534d 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 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author tomnl
date Wed, 02 May 2018 13:13:59 -0400
parents 7a95d9078691
children bf04ca943167
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
1 library(msPurity)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
2 library(optparse)
2
26fd52ed6d21 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
3 print(sessionInfo())
0
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
4
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
5 option_list <- list(
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
6 make_option(c("--mzML_file"), type="character"),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
7 make_option(c("--peaks_file"), type="character"),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
8 make_option(c("-o", "--out_dir"), type="character"),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
9 make_option("--minOffset", default=0.5),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
10 make_option("--maxOffset", default=0.5),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
11 make_option("--ilim", default=0.05),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
12 make_option("--ppm", default=4),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
13 make_option("--dimspy", action="store_true"),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
14 make_option("--sim", action="store_true"),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
15 make_option("--remove_nas", action="store_true"),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
16 make_option("--iwNorm", default="none", type="character"),
5
485c92d69777 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 2
diff changeset
17 make_option("--file_num_dimspy", default=1),
0
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
18 make_option("--exclude_isotopes", action="store_true"),
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
19 make_option("--isotope_matrix", type="character")
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
20 )
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
21
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
22 # store options
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
23 opt<- parse_args(OptionParser(option_list=option_list))
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
24
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
25 print(sessionInfo())
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
26 print(opt)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
27
5
485c92d69777 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 2
diff changeset
28 if (is.null(opt$dimspy)){
485c92d69777 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 2
diff changeset
29
485c92d69777 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 2
diff changeset
30 df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
485c92d69777 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 2
diff changeset
31 filename = NA
485c92d69777 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 2
diff changeset
32 }else{
0
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
33 indf <- read.table(opt$peaks_file,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
34 header = TRUE, sep='\t', stringsAsFactors = FALSE)
7
ef046d5e534d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents: 6
diff changeset
35
ef046d5e534d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents: 6
diff changeset
36 filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
0
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
37 # check if the data file is mzML or RAW (can only use mzML currently) so
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
38 # we expect an mzML file of the same name in the same folder
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
39 indf$i <- indf[,colnames(indf)==filename]
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
40 indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
41
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
42 filename = sub("raw", "mzML", filename, ignore.case = TRUE)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
43
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
44 df <- indf[4:nrow(indf),]
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
45 if ('blank_flag' %in% colnames(df)){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
46 df <- df[df$blank_flag==1,]
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
47 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
48
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
49 colnames(df)[colnames(df)=='m.z'] <- 'mz'
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
50
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
51 if ('nan' %in% df$mz){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
52 df[df$mz=='nan',]$mz <- NA
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
53 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
54 df$mz <- as.numeric(df$mz)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
55
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
56
5
485c92d69777 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 2
diff changeset
57
485c92d69777 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 2
diff changeset
58
0
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
59 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
60
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
61 if (!is.null(opt$remove_nas)){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
62 df <- df[!is.na(df$mz),]
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
63 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
64
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
65 if (is.null(opt$isotope_matrix)){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
66 im <- NULL
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
67 }else{
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
68 im <- read.table(opt$isotope_matrix,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
69 header = TRUE, sep='\t', stringsAsFactors = FALSE)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
70 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
71
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
72 if (is.null(opt$exclude_isotopes)){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
73 isotopes <- FALSE
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
74 }else{
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
75 isotopes <- TRUE
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
76 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
77
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
78
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
79 if (dir.exists(opt$mzML_file)){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
80 # if directory then we need to add a file name
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
81 print(filename)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
82 if (is.na(filename)){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
83 print('ERROR: If a directory is provided then a filename needs to be entered
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
84 directory or automatically obtained by using a dimspy output')
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
85 quit()
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
86 }else{
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
87 mzml_file <- file.path(opt$mzML_file, filename)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
88 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
89 }else{
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
90 mzml_file <- opt$mzML_file
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
91 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
92
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
93 if (is.null(opt$sim)){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
94 sim=FALSE
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
95 }else{
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
96 sim=TRUE
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
97 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
98
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
99 minOffset = as.numeric(opt$minOffset)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
100 maxOffset = as.numeric(opt$maxOffset)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
101
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
102
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
103
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
104 if (opt$iwNorm=='none'){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
105 iwNorm = FALSE
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
106 iwNormFun = NULL
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
107 }else if (opt$iwNorm=='gauss'){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
108 iwNorm = TRUE
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
109 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
110 }else if (opt$iwNorm=='rcosine'){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
111 iwNorm = TRUE
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
112 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
113 }else if (opt$iwNorm=='QE5'){
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
114 iwNorm = TRUE
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
115 iwNormFun = msPurity::iwNormQE.5()
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
116 }
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
117
6
7a95d9078691 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80
tomnl
parents: 5
diff changeset
118 print('FIRST ROWS OF PEAK FILE')
7a95d9078691 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80
tomnl
parents: 5
diff changeset
119 print(head(df))
0
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
120
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
121 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
122 filepth=mzml_file,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
123 minOffset=minOffset,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
124 maxOffset=maxOffset,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
125 ppm=opt$ppm,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
126 mzML=TRUE,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
127 sim = sim,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
128 ilim = opt$ilim,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
129 isotopes = isotopes,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
130 im = im,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
131 iwNorm = iwNorm,
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
132 iwNormFun = iwNormFun
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
133 )
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
134 predicted <- cbind(df, predicted)
b96fc0da0a32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
135
6
7a95d9078691 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80
tomnl
parents: 5
diff changeset
136 print(head(predicted))
7a95d9078691 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80
tomnl
parents: 5
diff changeset
137 print(file.path(opt$out_dir, 'anticipated_purity_dims.tsv'))
7a95d9078691 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80
tomnl
parents: 5
diff changeset
138 write.table(predicted, file.path(opt$out_dir, 'anticipated_purity_dims.tsv'), row.names=FALSE, sep='\t')