Mercurial > repos > computational-metabolomics > mspurity_createdatabase
view purityX.R @ 6:2f71b3495221 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author | computational-metabolomics |
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date | Thu, 04 Mar 2021 12:27:21 +0000 |
parents | f52287a06c02 |
children | efd14b326007 |
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library(msPurity) library(optparse) print(sessionInfo()) option_list <- list( make_option(c("--xset_path"), type = "character"), make_option(c("-o", "--out_dir"), type = "character"), make_option(c("--mzML_path"), type = "character"), make_option("--minOffset", default = 0.5), make_option("--maxOffset", default = 0.5), make_option("--ilim", default = 0.05), make_option("--iwNorm", default = "none", type = "character"), make_option("--exclude_isotopes", action = "store_true"), make_option("--isotope_matrix", type = "character"), make_option("--purityType", default = "purityFWHMmedian"), make_option("--singleFile", default = 0), make_option("--cores", default = 4), make_option("--xgroups", type = "character"), make_option("--rdata_name", default = "xset"), make_option("--camera_xcms", default = "xset"), make_option("--files", type = "character"), make_option("--galaxy_files", type = "character"), make_option("--choose_class", type = "character"), make_option("--ignore_files", type = "character"), make_option("--rtraw_columns", action = "store_true") ) opt <- parse_args(OptionParser(option_list = option_list)) print(opt) if (!is.null(opt$xgroups)) { xgroups <- as.numeric(strsplit(opt$xgroups, ",")[[1]]) }else{ xgroups <- NULL } print(xgroups) if (!is.null(opt$remove_nas)) { df <- df[!is.na(df$mz), ] } if (is.null(opt$isotope_matrix)) { im <- NULL }else{ im <- read.table(opt$isotope_matrix, header = TRUE, sep = "\t", stringsAsFactors = FALSE) } if (is.null(opt$exclude_isotopes)) { isotopes <- FALSE }else{ isotopes <- TRUE } if (is.null(opt$rtraw_columns)) { rtraw_columns <- FALSE }else{ rtraw_columns <- TRUE } loadRData <- function(rdata_path, xset_name) { #loads an RData file, and returns the named xset object if it is there load(rdata_path) return(get(ls()[ls() == xset_name])) } target_obj <- loadRData(opt$xset_path, opt$rdata_name) if (opt$camera_xcms == "camera") { xset <- target_obj@xcmsSet }else{ xset <- target_obj } print(xset) minOffset <- as.numeric(opt$minOffset) maxOffset <- as.numeric(opt$maxOffset) if (opt$iwNorm == "none") { iwNorm <- FALSE iwNormFun <- NULL }else if (opt$iwNorm == "gauss") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset) }else if (opt$iwNorm == "rcosine") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset) }else if (opt$iwNorm == "QE5") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormQE.5() } print(xset@filepaths) if (!is.null(opt$files)) { updated_filepaths <- trimws(strsplit(opt$files, ",")[[1]]) updated_filepaths <- updated_filepaths[updated_filepaths != ""] print(updated_filepaths) updated_filenames <- basename(updated_filepaths) original_filenames <- basename(xset@filepaths) update_idx <- match(updated_filenames, original_filenames) if (!is.null(opt$galaxy_files)) { galaxy_files <- trimws(strsplit(opt$galaxy_files, ",")[[1]]) galaxy_files <- galaxy_files[galaxy_files != ""] xset@filepaths <- galaxy_files[update_idx] }else{ xset@filepaths <- updated_filepaths[update_idx] } } if (!is.null(opt$choose_class)) { classes <- trimws(strsplit(opt$choose_class, ",")[[1]]) ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes) print("choose class") print(ignore_files_class) }else{ ignore_files_class <- NA } if (!is.null(opt$ignore_files)) { ignore_files_string <- trimws(strsplit(opt$ignore_files, ",")[[1]]) filenames <- rownames(xset@phenoData) ignore_files <- which(filenames %in% ignore_files_string) ignore_files <- unique(c(ignore_files, ignore_files_class)) ignore_files <- ignore_files[ignore_files != ""] }else{ if (anyNA(ignore_files_class)) { ignore_files <- NULL }else{ ignore_files <- ignore_files_class } } print("ignore_files") print(ignore_files) ppLCMS <- msPurity::purityX(xset = xset, offsets = c(minOffset, maxOffset), cores = opt$cores, xgroups = xgroups, purityType = opt$purityType, ilim = opt$ilim, isotopes = isotopes, im = im, iwNorm = iwNorm, iwNormFun = iwNormFun, singleFile = opt$singleFile, fileignore = ignore_files, rtrawColumns = rtraw_columns) dfp <- ppLCMS@predictions # to make compatable with deconrank colnames(dfp)[colnames(dfp) == "grpid"] <- "peakID" colnames(dfp)[colnames(dfp) == "median"] <- "medianPurity" colnames(dfp)[colnames(dfp) == "mean"] <- "meanPurity" colnames(dfp)[colnames(dfp) == "sd"] <- "sdPurity" colnames(dfp)[colnames(dfp) == "stde"] <- "sdePurity" colnames(dfp)[colnames(dfp) == "RSD"] <- "cvPurity" colnames(dfp)[colnames(dfp) == "pknm"] <- "pknmPurity" if (sum(is.na(dfp$medianPurity)) > 0) { dfp[is.na(dfp$medianPurity), ]$medianPurity <- 0 } print(head(dfp)) write.table(dfp, file.path(opt$out_dir, "purityX_output.tsv"), row.names = FALSE, sep = "\t") save.image(file.path(opt$out_dir, "purityX_output.RData"))