Mercurial > repos > computational-metabolomics > mspurity_createdatabase
view filterFragSpectra.R @ 8:efd14b326007 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author | computational-metabolomics |
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date | Wed, 12 Jun 2024 16:05:01 +0000 |
parents | 0cc6b67dccb8 |
children |
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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"), make_option("--allfrag", action = "store_true") ) 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 } if (is.null(opt$allfrag)) { opt$allfrag <- FALSE } else { opt$allfrag <- TRUE } pa <- filterFragSpectra(pa, ilim = opt$ilim, plim = opt$plim, ra = opt$ra, snr = opt$snr, rmp = opt$rmp, allfrag = opt$allfrag, snmeth = opt$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$subsetid <- seq_len(nrow(grpinfo)) result <- plyr::ddply(grpinfo, ~subsetid, setid, msms = msms) return(result) } # Set the relevant details setid <- function(grpinfo_i, msms) { msms_i <- msms[[1]][[grpinfo_i$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") } }