Mercurial > repos > tomnl > cameradims
changeset 9:ff054daae105 draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit fdaf9fc69c205ed76ef7cd82f4fa1624cf40419b-dirty
author | tomnl |
---|---|
date | Wed, 09 May 2018 09:26:12 -0400 |
parents | fe9a6e7bbebb |
children | 4b2ae555a5f8 |
files | flag-remove-peaks.R test-data/MERGED_multi_blank.rdata test-data/blank_check_b3.rdata test-data/multilist.tabular test-data/sampleList_choose_blank_xset.rdata |
diffstat | 5 files changed, 70 insertions(+), 12 deletions(-) [+] |
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--- a/flag-remove-peaks.R Fri May 04 10:26:13 2018 -0400 +++ b/flag-remove-peaks.R Wed May 09 09:26:12 2018 -0400 @@ -71,13 +71,20 @@ help="Assign True if files for each step saved (for testing purposes) [default = %default]" ), + make_option("--samplelist", type="character", help="Sample list to determine the blank class"), + make_option("--xset_name", default="xset", help="Name of the xcmsSet object within the RData file [default = %default]" ) + ) + #make_option("--multilist", action="store_true" + # help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist - sample list file has to be provided" + #), + # store options opt<- parse_args(OptionParser(option_list=option_list)) @@ -104,14 +111,31 @@ xset<-loadRData(opt$xset_path, opt$xset_name) print(xset) -ffrm_out <- XCMSwrapper::flag_remove(xset, +if (is.null(opt$samplelist)){ + blank_class <- opt$blank_class +}else{ + samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE) + samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes']) + + chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class] + if (length(chosen_blank)>1){ + print('ERROR: only 1 blank is currently allowed to be used with this tool') + exit() + } + blank_class <- as.character(chosen_blank) + print(blank_class) +} + + +if (is.null(opt$multilist)){ + ffrm_out <- XCMSwrapper::flag_remove(xset, pol=opt$polarity, rsd_i_blank=opt$rsd_i_blank, minfrac_blank=opt$minfrac_blank, rsd_rt_blank=opt$rsd_rt_blank, ithres_blank=opt$ithres_blank, s2b=opt$s2b, - ref.class=opt$blank_class, + ref.class=blank_class, egauss_thr=opt$egauss_thr, rsd_i_sample=opt$rsd_i_sample, minfrac_sample=opt$minfrac_sample, @@ -125,16 +149,36 @@ remove_spectra=remove_spectra, grp_rm_ids=unlist(strsplit(as.character(opt$grp_rm_ids), split=", "))[[1]]) -xset <- ffrm_out[[1]] -grp_peaklist <- ffrm_out[[2]] -removed_peaks <- ffrm_out[[3]] + xset <- ffrm_out[[1]] + grp_peaklist <- ffrm_out[[2]] + removed_peaks <- ffrm_out[[3]] + + save.image(file=file.path(opt$out_dir, 'xset_filtered.RData')) -save.image(file=file.path(opt$out_dir, 'xset_filtered.RData')) + # grpid needed for mspurity ID needed for deconrank... (will clean up at some up) + write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist), + file.path(opt$out_dir, 'peaklist_filtered.txt'), row.names=FALSE, sep='\t') + + removed_peaks <- data.frame(removed_peaks) + write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks), + file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t') + +}else{ -# grpid needed for mspurity ID needed for deconrank... (will clean up at some up) -write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist), - file.path(opt$out_dir, 'peaklist_filtered.txt'), row.names=FALSE, sep='\t') + + # TODO + #xsets <- split(xset, multilist_df$multlist) + # + #mult_grps <- unique(multilist_df$multlist) + # + #for (mgrp in mult_grps){ + # xset_i <- xsets[mgrp] + # xcms::group(xset_i, + # + # } -removed_peaks <- data.frame(removed_peaks) -write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks), - file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t') + + +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multilist.tabular Wed May 09 09:26:12 2018 -0400 @@ -0,0 +1,14 @@ +prefix sample_class multilist blank +Daph_P_WAX_2_LCMS-FC_Phenyl_neg_inj5_uWSp9ok s1 g1 no +Daph_P_WAX_2_LCMS-FC_Phenyl_neg_inj4_yWUsdrh s1 g1 no +Daph_P_WAX_2_LCMS-FC_Phenyl_neg_inj3 s2 g2 no +Daph_P_WAX_2_LCMS-FC_Phenyl_neg_inj2 s2 g2 no +Daph_P_WAX_2_LCMS-FC_Phenyl_neg_inj1_kdoZ9S6 s3 g3 no +Blank_P_WAX_2_LCMS-FC_Phenyl_neg_inj4 s3 g3 no +Blank_P_WAX_2_LCMS-FC_Phenyl_neg_inj3 b1 g1 yes +Blank_P_WAX_2_LCMS-FC_Phenyl_neg_inj2 b1 g1 yes +Blank_P_WAX_2_LCMS-FC_Phenyl_neg_inj1_J1u7Ldf b2 g2 yes +Daph_P_WAX_2_LCMSMS-FC_Phenyl_neg_inj4__incl2__2_t6HMnCz b2 g2 yes +Daph_P_WAX_2_LCMSMS-FC_Phenyl_neg_inj3__incl2__1_UFfCSXU b3 g3 yes +Daph_P_WAX_2_LCMSMS-FC_Phenyl_neg_inj2__incl1__2 b3 g3 yes +Daph_P_WAX_2_LCMSMS-FC_Phenyl_neg_inj1__incl1__1_Xci3Itv b3 g3 yes