Mercurial > repos > tomnl > anticipated_purity_lcms
view track_rt_raw.R @ 1:c64891642e41 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author | tomnl |
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date | Tue, 27 Mar 2018 05:32:57 -0400 |
parents | dc00b7222a3c |
children | b83bcc259b76 |
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library(optparse) library(xcms) option_list <- list( make_option(c("--xset_path"), type="character"), make_option(c("-o", "--out_dir"), type="character") ) # store options opt<- parse_args(OptionParser(option_list=option_list)) load(opt$xset_path) print(xset) rtraw <- xset@peaks[,c('rt', 'rtmin', 'rtmax')] colnames(rtraw) <- c('rt_raw','rtmin_raw','rtmax_raw') xset@peaks <- cbind(xset@peaks, rtraw) print('saving RData') save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData'))