Mercurial > repos > computational-metabolomics > mspurity_createdatabase
view filterFragSpectra.R @ 2:a11892cb997d draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
author | computational-metabolomics |
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date | Wed, 01 Apr 2020 11:17:09 -0400 |
parents | f52287a06c02 |
children | 2f71b3495221 |
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library(optparse) library(msPurity) library(xcms) print(sessionInfo()) option_list <- list( make_option("--out_rdata", type="character"), make_option("--out_peaklist_prec", type="character"), make_option("--out_peaklist_frag", type="character"), make_option("--pa", type="character"), make_option("--ilim", default=0.0), make_option("--plim", default=0.0), make_option("--ra", default=0.0), make_option("--snr", default=0.0), make_option("--rmp", action="store_true"), make_option("--snmeth", default="median", type="character") ) opt <- parse_args(OptionParser(option_list=option_list)) print(opt) loadRData <- function(rdata_path, name){ #loads an RData file, and returns the named xset object if it is there load(rdata_path) return(get(ls()[ls() %in% name])) } # Requires pa <- loadRData(opt$pa, 'pa') if(is.null(opt$rmp)){ opt$rmp = FALSE }else{ opt$rmp = TRUE } pa <- filterFragSpectra(pa, ilim=opt$ilim, plim=opt$plim, ra=opt$ra, snr=opt$snr, rmp=opt$rmp, snmeth=opt$snmeth) print(pa) save(pa, file=opt$out_rdata) # get the msms data for grpid from the purityA object msmsgrp <- function(grpid, pa){ msms <- pa@grped_ms2[grpid] grpinfo <- pa@grped_df[pa@grped_df$grpid==grpid,] grpinfo$subsetid <- 1:nrow(grpinfo) result <- plyr::ddply(grpinfo, ~subsetid, setid, msms=msms) return(result) } # Set the relevant details setid <- function(grpinfo_i, msms){ msms_i <- msms[[1]][[grpinfo_i$subsetid]] n <- nrow(msms_i) msms_i <- data.frame(msms_i) colnames(msms_i)[1:2] <- c('mz', 'i') m <- cbind('grpid'=rep(grpinfo_i$grpid,n), 'pid'=rep(grpinfo_i$pid,n), 'fileid'=rep(grpinfo_i$fileid,n), msms_i) return(m) } if (length(pa)>0){ if (length(pa@grped_ms2)==0){ message('No spectra available') } else{ # get group ids grpids <- unique(as.character(pa@grped_df$grpid)) # loop through all the group ids df_fragments = plyr::adply(grpids, 1, msmsgrp, pa=pa) df_fragments = merge(df_fragments, pa@puritydf[,c("pid", "acquisitionNum", "precursorScanNum")], by="pid") df_fragments = df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz),] #select and reorder columns df_fragments = df_fragments[,c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")] pa@grped_df$filename = sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)]) print(head(pa@grped_df)) write.table(pa@grped_df, opt$out_peaklist_prec, row.names=FALSE, sep='\t') print(head(df_fragments)) write.table(df_fragments, opt$out_peaklist_frag, row.names=FALSE, sep='\t') } }