Mercurial > repos > tomnl > flag_remove_peaks

annotate track_rt_raw.R @ 12:cb8dce9812ff 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 f79fa34772bbab836d89cf8bad52d49285409a98
author tomnl
date Thu, 14 Jun 2018 09:19:47 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
1 library(optparse)
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
2
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
3 print(sessionInfo())
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
4
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
5 option_list <- list(
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
6 make_option(c("--xset_path"), type="character"),
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
7 make_option(c("-o", "--out_dir"), type="character"),
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
8 make_option(c("--extract_peaks"), action="store_true")
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
9 )
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
10
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
11 # store options
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
12 opt<- parse_args(OptionParser(option_list=option_list))
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
13
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
14 load(opt$xset_path)
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
15
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
16 print(xset)
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
17
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
18 rtraw <- xset@peaks[,c('rt', 'rtmin', 'rtmax')]
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
19 colnames(rtraw) <- c('rt_raw','rtmin_raw','rtmax_raw')
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
20 xset@peaks <- cbind(xset@peaks, rtraw)
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
21
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
22
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
23 print('saving RData')
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
24 save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData'))
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
25
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
26 if(!is.null(opt$extract_peaks)){
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
27 write.table(xset@peaks, file.path(opt$out_dir, 'xset_peaks.tsv'), row.names=FALSE, sep='\t')
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
diff changeset
28 }