| Previous changeset 7:e9fbb65451f6 (2022-02-08) Next changeset 9:174a523cb1da (2024-06-13) |
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Commit message:
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 |
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modified:
README.rst averageFragSpectra.R combineAnnotations.R createDatabase.R createMSP.R dimsPredictPuritySingle.R filterFragSpectra.R flagRemove.R frag4feature.R macros.xml purityA.R purityX.R test-data/combineAnnotations_combined_annotations.sqlite test-data/combineAnnotations_combined_annotations.tsv test-data/purityX_output.tsv |
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added:
test-data/purityX_output.RData |
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removed:
test-data/purityX_output.Rdata |
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| diff -r e9fbb65451f6 -r cb4aeec93d49 README.rst --- a/README.rst Tue Feb 08 14:04:07 2022 +0000 +++ b/README.rst Wed Jun 12 16:08:23 2024 +0000 |
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| @@ -1,15 +1,15 @@ msPurity for Galaxy ======================== -|Build Status (Travis)| |Git| |Bioconda| |License| +|Git| |Bioconda| |License| -Version v1.16.2+galaxy1 +Version v1.16.2+galaxy2 ------------------------ - msPurity - bioconductor-mspurity v1.16.2 - Galaxy tools - - v1 + - v2 About ------ @@ -54,6 +54,13 @@ Changes ------------------------- +v1.16.2-galaxy2 + - Fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53) + - Cleanup of xml based on updated lint requirements + - Fix combineAnnotation tests + - Cleanup of repository folders + - github actions temp update (lintr removed) + v1.16.2-galaxy1 - Fix for "scan" option for spectral matching - Add allfrag option for filterFragSpectra |
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| diff -r e9fbb65451f6 -r cb4aeec93d49 averageFragSpectra.R --- a/averageFragSpectra.R Tue Feb 08 14:04:07 2022 +0000 +++ b/averageFragSpectra.R Wed Jun 12 16:08:23 2024 +0000 |
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| @@ -5,30 +5,28 @@ get_av_spectra <- function(x) { - if (length(x$av_intra) > 0) { av_intra_df <- plyr::ldply(x$av_intra) if (nrow(av_intra_df) == 0) { av_intra_df <- NULL - }else{ + } else { av_intra_df$method <- "intra" } - - }else{ + } else { av_intra_df <- NULL } if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) { av_inter_df <- NULL - }else{ + } else { av_inter_df <- x$av_inter av_inter_df$method <- "inter" } if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) { av_all_df <- NULL - }else{ + } else { av_all_df <- x$av_all av_all_df$method <- "all" } @@ -60,9 +58,9 @@ load_r_data <- function(rdata_path, name) { - #loads an RData file, and returns the named xset object if it is there - load(rdata_path) - return(get(ls()[ls() %in% name])) + # loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() %in% name])) } # Requires @@ -72,59 +70,58 @@ if (is.null(opt$rmp)) { rmp <- FALSE -}else{ +} else { rmp <- TRUE } if (is.null(opt$sumi)) { sumi <- FALSE -}else{ +} else { sumi <- TRUE } if (opt$av_level == "intra") { pa <- msPurity::averageIntraFragSpectra(pa, - minfrac = opt$minfrac, - minnum = opt$minnum, - ppm = opt$ppm, - snr = opt$snr, - ra = opt$ra, - av = opt$av, - sumi = sumi, - rmp = rmp, - cores = opt$cores) - + minfrac = opt$minfrac, + minnum = opt$minnum, + ppm = opt$ppm, + snr = opt$snr, + ra = opt$ra, + av = opt$av, + sumi = sumi, + rmp = rmp, + cores = opt$cores + ) } else if (opt$av_level == "inter") { - pa <- msPurity::averageInterFragSpectra(pa, - minfrac = opt$minfrac, - minnum = opt$minnum, - ppm = opt$ppm, - snr = opt$snr, - ra = opt$ra, - av = opt$av, - sumi = sumi, - rmp = rmp, - cores = opt$cores) + minfrac = opt$minfrac, + minnum = opt$minnum, + ppm = opt$ppm, + snr = opt$snr, + ra = opt$ra, + av = opt$av, + sumi = sumi, + rmp = rmp, + cores = opt$cores + ) } else if (opt$av_level == "all") { - pa <- msPurity::averageAllFragSpectra(pa, - minfrac = opt$minfrac, - minnum = opt$minnum, - ppm = opt$ppm, - snr = opt$snr, - ra = opt$ra, - av = opt$av, - sumi = sumi, - rmp = rmp, - cores = opt$cores) + minfrac = opt$minfrac, + minnum = opt$minnum, + ppm = opt$ppm, + snr = opt$snr, + ra = opt$ra, + av = opt$av, + sumi = sumi, + rmp = rmp, + cores = opt$cores + ) } print(pa) save(pa, file = opt$out_rdata) if (length(pa) > 0) { - av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra) if (nrow(av_spectra) == 0) { @@ -138,18 +135,20 @@ colnames(av_spectra)[2] <- "fileid" av_spectra$avid <- seq_len(nrow(av_spectra)) - filenames <- sapply(av_spectra$fileid, - function(x) names(pa@fileList)[as.integer(x)]) + filenames <- sapply( + av_spectra$fileid, + function(x) names(pa@fileList)[as.integer(x)] + ) # filenames_galaxy <- sapply( # av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)])) - av_spectra <- as.data.frame( - append(av_spectra, list(filename = filenames), after = 2)) + av_spectra <- as.data.frame( + append(av_spectra, list(filename = filenames), after = 2) + ) } print(head(av_spectra)) write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t") - } } |
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| diff -r e9fbb65451f6 -r cb4aeec93d49 combineAnnotations.R --- a/combineAnnotations.R Tue Feb 08 14:04:07 2022 +0000 +++ b/combineAnnotations.R Wed Jun 12 16:08:23 2024 +0000 |
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| @@ -9,23 +9,18 @@ make_option(c("-c", "--sirius_csi_resultPth"), type = "character"), make_option(c("-p", "--probmetab_resultPth"), type = "character"), make_option(c("-l", "--ms1_lookup_resultPth"), type = "character"), - make_option("--ms1_lookup_checkAdducts", action = "store_true"), make_option("--ms1_lookup_keepAdducts", type = "character", default = NA), make_option("--ms1_lookup_dbSource", type = "character", default = "hmdb"), - make_option("--sm_weight", type = "numeric"), make_option("--metfrag_weight", type = "numeric"), make_option("--sirius_csi_weight", type = "numeric"), make_option("--probmetab_weight", type = "numeric"), make_option("--ms1_lookup_weight", type = "numeric"), make_option("--biosim_weight", type = "numeric"), - make_option("--summaryOutput", action = "store_true"), - make_option("--create_new_database", action = "store_true"), make_option("--outdir", type = "character", default = "."), - make_option("--compoundDbType", type = "character", default = "sqlite"), make_option("--compoundDbPth", type = "character", default = NA), make_option("--compoundDbHost", type = "character", default = NA) @@ -37,7 +32,7 @@ if (!is.null(opt$create_new_database)) { sm_resultPth <- file.path(opt$outdir, "combined_annotations.sqlite") file.copy(opt$sm_resultPth, sm_resultPth) -}else{ +} else { sm_resultPth <- opt$sm_resultPth } @@ -45,18 +40,19 @@ opt$ms1_lookup_checkAdducts <- FALSE } if (!is.null(opt$ms1_lookup_keepAdducts)) { - opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts) - opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts) - ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]] + opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts) + opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts) + ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]] } -weights <- list("sm" = opt$sm_weight, - "metfrag" = opt$metfrag_weight, - "sirius_csifingerid" = opt$sirius_csi_weight, - "probmetab" = opt$probmetab_weight, - "ms1_lookup" = opt$ms1_lookup_weight, - "biosim" = opt$biosim_weight - ) +weights <- list( + "sm" = opt$sm_weight, + "metfrag" = opt$metfrag_weight, + "sirius_csifingerid" = opt$sirius_csi_weight, + "probmetab" = opt$probmetab_weight, + "ms1_lookup" = opt$ms1_lookup_weight, + "biosim" = opt$biosim_weight +) print(weights) if (is.null(opt$probmetab_resultPth)) { @@ -69,8 +65,8 @@ if (is.null(opt$summaryOutput)) { summaryOutput <- FALSE -}else{ - summaryOutput <- TRUE +} else { + summaryOutput <- TRUE } if (opt$compoundDbType == "local_config") { @@ -82,7 +78,7 @@ source(paste(base_dir, fname, sep = "/")) } source_local("dbconfig.R") -}else{ +} else { compoundDbPth <- opt$compoundDbPth compoundDbType <- opt$compoundDbType compoundDbName <- NA @@ -93,31 +89,33 @@ } summary_output <- msPurity::combineAnnotations( - sm_resultPth = sm_resultPth, - compoundDbPth = compoundDbPth, - metfrag_resultPth = opt$metfrag_resultPth, - sirius_csi_resultPth = opt$sirius_csi_resultPth, - probmetab_resultPth = opt$probmetab_resultPth, - ms1_lookup_resultPth = opt$ms1_lookup_resultPth, - ms1_lookup_keepAdducts = ms1_lookup_keepAdducts, - ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts, - - compoundDbType = compoundDbType, - compoundDbName = compoundDbName, - compoundDbHost = compoundDbHost, - compoundDbPort = compoundDbPort, - compoundDbUser = compoundDbUser, - compoundDbPass = compoundDbPass, - weights = weights, - summaryOutput = summaryOutput) + sm_resultPth = sm_resultPth, + compoundDbPth = compoundDbPth, + metfrag_resultPth = opt$metfrag_resultPth, + sirius_csi_resultPth = opt$sirius_csi_resultPth, + probmetab_resultPth = opt$probmetab_resultPth, + ms1_lookup_resultPth = opt$ms1_lookup_resultPth, + ms1_lookup_keepAdducts = ms1_lookup_keepAdducts, + ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts, + compoundDbType = compoundDbType, + compoundDbName = compoundDbName, + compoundDbHost = compoundDbHost, + compoundDbPort = compoundDbPort, + compoundDbUser = compoundDbUser, + compoundDbPass = compoundDbPass, + weights = weights, + summaryOutput = summaryOutput +) if (summaryOutput) { write.table(summary_output, - file.path(opt$outdir, "combined_annotations.tsv"), - sep = "\t", row.names = FALSE) + file.path(opt$outdir, "combined_annotations.tsv"), + sep = "\t", row.names = FALSE + ) } write.table(summary_output, - file.path(opt$outdir, "combined_annotations.tsv"), - sep = "\t", row.names = FALSE) + file.path(opt$outdir, "combined_annotations.tsv"), + sep = "\t", row.names = FALSE +) closeAllConnections() |
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| diff -r e9fbb65451f6 -r cb4aeec93d49 createDatabase.R --- a/createDatabase.R Tue Feb 08 14:04:07 2022 +0000 +++ b/createDatabase.R Wed Jun 12 16:08:23 2024 +0000 |
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| @@ -6,7 +6,6 @@ print("CREATING DATABASE") xset_pa_filename_fix <- function(opt, pa, xset) { - if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) { # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables # needs to be done due to Galaxy moving the files around and screwing up any links to files @@ -18,7 +17,7 @@ galaxy_names <- galaxy_names[galaxy_names != ""] nsave <- names(pa@fileList) - old_filenames <- basename(pa@fileList) + old_filenames <- basename(pa@fileList) pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] names(pa@fileList) <- nsave @@ -27,12 +26,12 @@ } - if (!all(basename(pa@fileList) == basename(xset@filepaths))) { + if (!all(basename(pa@fileList) == basename(xset@filepaths))) { if (!all(names(pa@fileList) == basename(xset@filepaths))) { - print("FILELISTS DO NOT MATCH") - message("FILELISTS DO NOT MATCH") - quit(status = 1) - }else{ + print("FILELISTS DO NOT MATCH") + message("FILELISTS DO NOT MATCH") + quit(status = 1) + } else { xset@filepaths <- unname(pa@fileList) } } @@ -64,22 +63,23 @@ print(opt) loadRData <- function(rdata_path, name) { -#loads an RData file, and returns the named xset object if it is there - load(rdata_path) - return(get(ls()[ls() %in% name])) + # loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() %in% name])) } getxcmsSetObject <- function(xobject) { - # XCMS 1.x - if (class(xobject) == "xcmsSet") - return(xobject) - # XCMS 3.x - if (class(xobject) == "XCMSnExp") { - # Get the legacy xcmsSet object - suppressWarnings(xset <- as(xobject, "xcmsSet")) - xcms::sampclass(xset) <- xset@phenoData$sample_group - return(xset) - } + # XCMS 1.x + if (class(xobject) == "xcmsSet") { + return(xobject) + } + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, "xcmsSet")) + xcms::sampclass(xset) <- xset@phenoData$sample_group + return(xset) + } } @@ -96,19 +96,17 @@ # Missing list element causes failures (should be updated # in msPurity R package for future releases) if (!exists("allfrag", where = pa@filter_frag_params)) { - pa@filter_frag_params$allfrag <- FALSE + pa@filter_frag_params$allfrag <- FALSE } if (opt$xcms_camera_option == "xcms") { - xset <- loadRData(opt$xset, c("xset", "xdata")) xset <- getxcmsSetObject(xset) fix <- xset_pa_filename_fix(opt, pa, xset) pa <- fix[[1]] xset <- fix[[2]] xa <- NULL -}else{ - +} else { xa <- loadRData(opt$xset, "xa") fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet) pa <- fix[[1]] @@ -119,16 +117,16 @@ if (is.null(opt$grpPeaklist)) { grpPeaklist <- NA -}else{ +} else { grpPeaklist <- opt$grpPeaklist } dbPth <- msPurity::createDatabase(pa, - xset = xset, - xsa = xa, - outDir = opt$outDir, - grpPeaklist = grpPeaklist, - dbName = "createDatabase_output.sqlite" + xset = xset, + xsa = xa, + outDir = opt$outDir, + grpPeaklist = grpPeaklist, + dbName = "createDatabase_output.sqlite" ) @@ -136,9 +134,8 @@ if (!is.null(opt$eic)) { - if (is.null(xset)) { - xset <- xa@xcmsSet + xset <- xa@xcmsSet } # previous check should have matched filelists together xset@filepaths <- unname(pa@fileList) @@ -150,19 +147,19 @@ x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])] x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])] return(x) - } xset@peaks <- as.matrix( - plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset = xset)) + plyr::ddply(data.frame(xset@peaks), ~sample, convert2Raw, xset = xset) + ) # Saves the EICS into the previously created database px <- msPurity::purityX(xset, - saveEIC = TRUE, - cores = 1, - sqlitePth = dbPth, - rtrawColumns = TRUE) - + saveEIC = TRUE, + cores = 1, + sqlitePth = dbPth, + rtrawColumns = TRUE + ) } closeAllConnections() |
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| diff -r e9fbb65451f6 -r cb4aeec93d49 createMSP.R --- a/createMSP.R Tue Feb 08 14:04:07 2022 +0000 +++ b/createMSP.R Wed Jun 12 16:08:23 2024 +0000 |
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| @@ -26,59 +26,58 @@ if (is.null(opt$metadata)) { metadata <- NULL -}else{ - metadata <- read.table(opt$metadata, header = TRUE, sep = "\t", - stringsAsFactors = FALSE, check.names = FALSE) +} else { + metadata <- read.table(opt$metadata, + header = TRUE, sep = "\t", + stringsAsFactors = FALSE, check.names = FALSE + ) if (!opt$metadata_cols_filter == "") { - metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]] + metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]] - metadata <- metadata[, metadata_cols_filter, drop = FALSE] - print(metadata) + metadata <- metadata[, metadata_cols_filter, drop = FALSE] + print(metadata) - if (!"grpid" %in% colnames(metadata)) { - metadata$grpid <- seq_len(nrow(metadata)) - } + if (!"grpid" %in% colnames(metadata)) { + metadata$grpid <- seq_len(nrow(metadata)) + } - print(metadata) - + print(metadata) } - } if (is.null(opt$metadata_cols) || opt$metadata_cols == "") { - metadata_cols <- NULL -}else{ - metadata_cols <- opt$metadata_cols - + metadata_cols <- NULL +} else { + metadata_cols <- opt$metadata_cols } if (is.null(opt$adduct_split)) { adduct_split <- FALSE -}else{ +} else { adduct_split <- TRUE } if (is.null(opt$xcms_groupids)) { xcms_groupids <- NULL -}else{ +} else { xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ",")[[1]]) } if (is.null(opt$include_adducts_custom)) { include_adducts_custom <- "" -}else{ +} else { include_adducts_custom <- opt$include_adducts_custom } if (opt$include_adducts == "None") { include_adducts <- "" -}else{ +} else { include_adducts <- opt$include_adducts } @@ -96,22 +95,23 @@ if (is.null(opt$filter)) { filter <- FALSE -}else{ +} else { filter <- TRUE } msPurity::createMSP(pa, - msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"), - metadata = metadata, - metadata_cols = metadata_cols, - method = opt$method, - adduct_split = adduct_split, - xcms_groupids = xcms_groupids, - filter = filter, - intensity_ra = opt$intensity_ra, - include_adducts = include_adducts_all, - msp_schema = opt$msp_schema) + msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"), + metadata = metadata, + metadata_cols = metadata_cols, + method = opt$method, + adduct_split = adduct_split, + xcms_groupids = xcms_groupids, + filter = filter, + intensity_ra = opt$intensity_ra, + include_adducts = include_adducts_all, + msp_schema = opt$msp_schema +) -print("msp created") +print("msp created") \ No newline at end of file |
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| diff -r e9fbb65451f6 -r cb4aeec93d49 dimsPredictPuritySingle.R --- a/dimsPredictPuritySingle.R Tue Feb 08 14:04:07 2022 +0000 +++ b/dimsPredictPuritySingle.R Wed Jun 12 16:08:23 2024 +0000 |
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| @@ -3,23 +3,23 @@ print(sessionInfo()) option_list <- list( - make_option(c("--mzML_file"), type = "character"), - make_option(c("--mzML_files"), type = "character"), - make_option(c("--mzML_filename"), type = "character", default = ""), - make_option(c("--mzML_galaxy_names"), type = "character", default = ""), - make_option(c("--peaks_file"), type = "character"), - make_option(c("-o", "--out_dir"), type = "character"), - make_option("--minoffset", default = 0.5), - make_option("--maxoffset", default = 0.5), - make_option("--ilim", default = 0.05), - make_option("--ppm", default = 4), - make_option("--dimspy", action = "store_true"), - make_option("--sim", action = "store_true"), - make_option("--remove_nas", action = "store_true"), - make_option("--iwNorm", default = "none", type = "character"), - make_option("--file_num_dimspy", default = 1), - make_option("--exclude_isotopes", action = "store_true"), - make_option("--isotope_matrix", type = "character") + make_option(c("--mzML_file"), type = "character"), + make_option(c("--mzML_files"), type = "character"), + make_option(c("--mzML_filename"), type = "character", default = ""), + make_option(c("--mzML_galaxy_names"), type = "character", default = ""), + make_option(c("--peaks_file"), type = "character"), + make_option(c("-o", "--out_dir"), type = "character"), + make_option("--minoffset", default = 0.5), + make_option("--maxoffset", default = 0.5), + make_option("--ilim", default = 0.05), + make_option("--ppm", default = 4), + make_option("--dimspy", action = "store_true"), + make_option("--sim", action = "store_true"), + make_option("--remove_nas", action = "store_true"), + make_option("--iwNorm", default = "none", type = "character"), + make_option("--file_num_dimspy", default = 1), + make_option("--exclude_isotopes", action = "store_true"), + make_option("--isotope_matrix", type = "character") ) # store options @@ -43,7 +43,7 @@ galaxy_names <- str_to_vec(galaxy_names) if (mzML_filename %in% galaxy_names) { return(mzML_files[galaxy_names == mzML_filename]) - }else{ + } else { stop(paste("mzML file not found - ", mzML_filename)) } } @@ -53,15 +53,18 @@ df <- read.table(opt$peaks_file, header = TRUE, sep = "\t") if (file.exists(opt$mzML_file)) { mzML_file <- opt$mzML_file - }else if (!is.null(opt$mzML_files)) { - mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, - opt$mzML_filename) - }else{ + } else if (!is.null(opt$mzML_files)) { + mzML_file <- find_mzml_file( + opt$mzML_files, opt$mzML_galaxy_names, + opt$mzML_filename + ) + } else { mzML_file <- file.path(opt$mzML_file, filename) } -}else{ +} else { indf <- read.table(opt$peaks_file, - header = TRUE, sep = "\t", stringsAsFactors = FALSE) + header = TRUE, sep = "\t", stringsAsFactors = FALSE + ) filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy] print(filename) @@ -75,9 +78,9 @@ if (file.exists(opt$mzML_file)) { mzML_file <- opt$mzML_file - }else if (!is.null(opt$mzML_files)) { + } else if (!is.null(opt$mzML_files)) { mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename) - }else{ + } else { mzML_file <- file.path(opt$mzML_file, filename) } @@ -95,25 +98,26 @@ } if (!is.null(opt$remove_nas)) { - df <- df[!is.na(df$mz), ] + df <- df[!is.na(df$mz), ] } if (is.null(opt$isotope_matrix)) { im <- NULL -}else{ +} else { im <- read.table(opt$isotope_matrix, - header = TRUE, sep = "\t", stringsAsFactors = FALSE) + header = TRUE, sep = "\t", stringsAsFactors = FALSE + ) } if (is.null(opt$exclude_isotopes)) { isotopes <- FALSE -}else{ +} else { isotopes <- TRUE } if (is.null(opt$sim)) { sim <- FALSE -}else{ +} else { sim <- TRUE } @@ -123,13 +127,13 @@ if (opt$iwNorm == "none") { iwNorm <- FALSE iwNormFun <- NULL -}else if (opt$iwNorm == "gauss") { +} else if (opt$iwNorm == "gauss") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset) -}else if (opt$iwNorm == "rcosine") { +} else if (opt$iwNorm == "rcosine") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset) -}else if (opt$iwNorm == "QE5") { +} else if (opt$iwNorm == "QE5") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormQE.5() } @@ -138,23 +142,24 @@ print(head(df)) print(mzML_file) predicted <- msPurity::dimsPredictPuritySingle(df$mz, - filepth = mzML_file, - minOffset = minOffset, - maxOffset = maxOffset, - ppm = opt$ppm, - mzML = TRUE, - sim = sim, - ilim = opt$ilim, - isotopes = isotopes, - im = im, - iwNorm = iwNorm, - iwNormFun = iwNormFun - ) + filepth = mzML_file, + minOffset = minOffset, + maxOffset = maxOffset, + ppm = opt$ppm, + mzML = TRUE, + sim = sim, + ilim = opt$ilim, + isotopes = isotopes, + im = im, + iwNorm = iwNorm, + iwNormFun = iwNormFun +) predicted <- cbind(df, predicted) print(head(predicted)) print(file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv")) write.table(predicted, - file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"), - row.names = FALSE, sep = "\t") + file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"), + row.names = FALSE, sep = "\t" +) |
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| diff -r e9fbb65451f6 -r cb4aeec93d49 filterFragSpectra.R --- a/filterFragSpectra.R Tue Feb 08 14:04:07 2022 +0000 +++ b/filterFragSpectra.R Wed Jun 12 16:08:23 2024 +0000 |
| [ |
| @@ -9,13 +9,10 @@ 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") @@ -26,9 +23,9 @@ 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])) + # loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() %in% name])) } # Requires @@ -36,24 +33,25 @@ if (is.null(opt$rmp)) { opt$rmp <- FALSE -}else{ +} else { opt$rmp <- TRUE } if (is.null(opt$allfrag)) { opt$allfrag <- FALSE -}else{ +} else { opt$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$snmeth) + ilim = opt$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$out_rdata) @@ -82,11 +80,9 @@ if (length(pa) > 0) { - if (length(pa@grped_ms2) == 0) { message("No spectra available") } else { - # get group ids grpids <- unique(as.character(pa@grped_df$grpid)) @@ -94,7 +90,7 @@ 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$mz), ] - #select and reorder columns + # select and reorder columns df_fragments <- df_fragments[, c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")] pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)]) |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 flagRemove.R --- a/flagRemove.R Tue Feb 08 14:04:07 2022 +0000 +++ b/flagRemove.R Wed Jun 12 16:08:23 2024 +0000 |
| [ |
| b'@@ -2,77 +2,93 @@\n library(optparse)\n print(sessionInfo())\n option_list <- list(\n- make_option(c("-o", "--out_dir"), type = "character", default = getwd(),\n- help = "Output folder for resulting files [default = %default]"\n- ),\n- make_option(c("-x", "--xset_path"), type = "character", default = file.path(getwd(), "xset.rds"),\n- help = "The path to the xcmsSet object [default = %default]"\n- ),\n- make_option("--polarity", default = NA,\n- help = "polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"\n- ),\n- make_option("--rsd_i_blank", default = 100,\n- help = "RSD threshold for the blank [default = %default]"\n- ),\n- make_option("--minfrac_blank", default = 0.5,\n- help = "minimum fraction of files for features needed for the blank [default = %default]"\n- ),\n- make_option("--rsd_rt_blank", default = 100,\n- help = "RSD threshold for the RT of the blank [default = %default]"\n- ),\n-\n- make_option("--ithres_blank", default = 0,\n- help = "Intensity threshold for the blank [default = %default]"\n- ),\n- make_option("--s2b", default = 10,\n- help = "fold change (sample/blank) needed for sample peak to be allowed. e.g.\n+ make_option(c("-o", "--out_dir"),\n+ type = "character", default = getwd(),\n+ help = "Output folder for resulting files [default = %default]"\n+ ),\n+ make_option(c("-x", "--xset_path"),\n+ type = "character", default = file.path(getwd(), "xset.rds"),\n+ help = "The path to the xcmsSet object [default = %default]"\n+ ),\n+ make_option("--polarity",\n+ default = NA,\n+ help = "polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"\n+ ),\n+ make_option("--rsd_i_blank",\n+ default = 100,\n+ help = "RSD threshold for the blank [default = %default]"\n+ ),\n+ make_option("--minfrac_blank",\n+ default = 0.5,\n+ help = "minimum fraction of files for features needed for the blank [default = %default]"\n+ ),\n+ make_option("--rsd_rt_blank",\n+ default = 100,\n+ help = "RSD threshold for the RT of the blank [default = %default]"\n+ ),\n+ make_option("--ithres_blank",\n+ default = 0,\n+ help = "Intensity threshold for the blank [default = %default]"\n+ ),\n+ make_option("--s2b",\n+ default = 10,\n+ help = "fold change (sample/blank) needed for sample peak to be allowed. e.g.\n if s2b set to 10 and the recorded sample \'intensity\' value was 100 and blank was 10.\n 1000/10 = 100, so sample has fold change higher than the threshold and the peak\n is not considered a blank [default = %default]"\n- ),\n- make_option("--blank_class", default = "blank", type = "character",\n- help = "A string representing the class that will be used for the blank.[default = %default]"\n- ),\n- make_option("--egauss_thr", default = NA,\n- help = "Threshold for filtering out non gaussian shaped peaks. Note this only works\n+ ),\n+ make_option("--blank_class",\n+ default = "blank", type = "character",\n+ help = "A string representing the class that will be used for the blank.[default = %default]"\n+ ),\n+ make_option("--egauss_thr",\n+ default = NA,\n+ help = "Threshold for filtering out non gaussian shaped peaks. Note this only works\n if the \'verbose columns\' and \'fit gauss\' was used with xcms\n [default = %default]"\n- ),\n- make_option("--rsd_i_sample", default = 100,\n- help = "RSD threshold for the samples [default = %default]"\n- ),\n- make_option("--minfrac_sample", default = 0.8,\n- help = "minimum fraction of files for features needed for the samples [default = %default]"\n- ),\n- make_option("--rsd_rt_sample", default = 10'..b' # XCMS 1.x\n- if (class(xobject) == "xcmsSet")\n+ if (class(xobject) == "xcmsSet") {\n return(xobject)\n+ }\n # XCMS 3.x\n if (class(xobject) == "XCMSnExp") {\n # Get the legacy xcmsSet object\n@@ -116,7 +133,7 @@\n \n \n loadRData <- function(rdata_path, name) {\n-#loads an RData file, and returns the named xset object if it is there\n+ # loads an RData file, and returns the named xset object if it is there\n load(rdata_path)\n return(get(ls()[ls() %in% name]))\n }\n@@ -126,7 +143,7 @@\n print(xset)\n if (is.null(opt$samplelist)) {\n blank_class <- opt$blank_class\n-}else{\n+} else {\n samplelist <- read.table(opt$samplelist, sep = "\\t", header = TRUE)\n samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"])\n \n@@ -142,25 +159,26 @@\n \n if (is.null(opt$multilist)) {\n ffrm_out <- flag_remove(xset,\n- pol = opt$polarity,\n- rsd_i_blank = opt$rsd_i_blank,\n- minfrac_blank = opt$minfrac_blank,\n- rsd_rt_blank = opt$rsd_rt_blank,\n- ithres_blank = opt$ithres_blank,\n- s2b = opt$s2b,\n- ref.class = blank_class,\n- egauss_thr = opt$egauss_thr,\n- rsd_i_sample = opt$rsd_i_sample,\n- minfrac_sample = opt$minfrac_sample,\n- rsd_rt_sample = opt$rsd_rt_sample,\n- ithres_sample = opt$ithres_sample,\n- minfrac_xcms = opt$minfrac_xcms,\n- mzwid = opt$mzwid,\n- bw = opt$bw,\n- out_dir = opt$out_dir,\n- temp_save = temp_save,\n- remove_spectra = remove_spectra,\n- grp_rm_ids = unlist(strsplit(as.character(opt$grp_rm_ids), split = ", "))[[1]])\n+ pol = opt$polarity,\n+ rsd_i_blank = opt$rsd_i_blank,\n+ minfrac_blank = opt$minfrac_blank,\n+ rsd_rt_blank = opt$rsd_rt_blank,\n+ ithres_blank = opt$ithres_blank,\n+ s2b = opt$s2b,\n+ ref.class = blank_class,\n+ egauss_thr = opt$egauss_thr,\n+ rsd_i_sample = opt$rsd_i_sample,\n+ minfrac_sample = opt$minfrac_sample,\n+ rsd_rt_sample = opt$rsd_rt_sample,\n+ ithres_sample = opt$ithres_sample,\n+ minfrac_xcms = opt$minfrac_xcms,\n+ mzwid = opt$mzwid,\n+ bw = opt$bw,\n+ out_dir = opt$out_dir,\n+ temp_save = temp_save,\n+ remove_spectra = remove_spectra,\n+ grp_rm_ids = unlist(strsplit(as.character(opt$grp_rm_ids), split = ", "))[[1]]\n+ )\n print("flag remove finished")\n xset <- ffrm_out[[1]]\n grp_peaklist <- ffrm_out[[2]]\n@@ -172,26 +190,26 @@\n peak_pth <- file.path(opt$out_dir, "peaklist_filtered.tsv")\n print(peak_pth)\n write.table(data.frame("grpid" = rownames(grp_peaklist), "ID" = rownames(grp_peaklist), grp_peaklist),\n- peak_pth, row.names = FALSE, sep = "\\t")\n+ peak_pth,\n+ row.names = FALSE, sep = "\\t"\n+ )\n \n removed_peaks <- data.frame(removed_peaks)\n write.table(data.frame("ID" = rownames(removed_peaks), removed_peaks),\n- file.path(opt$out_dir, "removed_peaks.tsv"), row.names = FALSE, sep = "\\t")\n-\n-}else{\n-\n- # nolint start\n- # TODO\n- #xsets <- split(xset, multilist_df$multlist)\n- #\n- #mult_grps <- unique(multilist_df$multlist)\n- #\n- #for (mgrp in mult_grps){\n- # xset_i <- xsets[mgrp]\n- # xcms::group(xset_i,\n- #\n- # }\n- # nolint end\n-\n-\n+ file.path(opt$out_dir, "removed_peaks.tsv"),\n+ row.names = FALSE, sep = "\\t"\n+ )\n+} else {\n+ # nolint start\n+ # TODO\n+ # xsets <- split(xset, multilist_df$multlist)\n+ #\n+ # mult_grps <- unique(multilist_df$multlist)\n+ #\n+ # for (mgrp in mult_grps){\n+ # xset_i <- xsets[mgrp]\n+ # xcms::group(xset_i,\n+ #\n+ # }\n+ # nolint end\n }\n' |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 frag4feature.R --- a/frag4feature.R Tue Feb 08 14:04:07 2022 +0000 +++ b/frag4feature.R Wed Jun 12 16:08:23 2024 +0000 |
| [ |
| @@ -3,64 +3,61 @@ library(xcms) print(sessionInfo()) -xset_pa_filename_fix <- function(opt, pa, xset=NULL) { - +xset_pa_filename_fix <- function(opt, pa, xset = NULL) { + if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) { + # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables + # needs to be done due to Galaxy moving the files around and screwing up any links to files - if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) { - # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables - # needs to be done due to Galaxy moving the files around and screwing up any links to files + filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) # nolint - filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) # nolint + filepaths <- filepaths[filepaths != ""] - filepaths <- filepaths[filepaths != ""] - - galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]]) - galaxy_names <- galaxy_names[galaxy_names != ""] + galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]]) + galaxy_names <- galaxy_names[galaxy_names != ""] - nsave <- names(pa@fileList) - old_filenames <- basename(pa@fileList) + nsave <- names(pa@fileList) + old_filenames <- basename(pa@fileList) - pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] - names(pa@fileList) <- nsave + pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] + names(pa@fileList) <- nsave - pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) - pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) - } - print(pa@fileList) + pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) + pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) + } + print(pa@fileList) - if (!is.null(xset)) { - - print(xset@filepaths) + if (!is.null(xset)) { + print(xset@filepaths) - if (!all(basename(pa@fileList) == basename(xset@filepaths))) { - if (!all(names(pa@fileList) == basename(xset@filepaths))) { - print("FILELISTS DO NOT MATCH") - message("FILELISTS DO NOT MATCH") - quit(status = 1) - }else{ - xset@filepaths <- unname(pa@fileList) - } - } - } + if (!all(basename(pa@fileList) == basename(xset@filepaths))) { + if (!all(names(pa@fileList) == basename(xset@filepaths))) { + print("FILELISTS DO NOT MATCH") + message("FILELISTS DO NOT MATCH") + quit(status = 1) + } else { + xset@filepaths <- unname(pa@fileList) + } + } + } - return(list(pa, xset)) + return(list(pa, xset)) } option_list <- list( - make_option(c("-o", "--out_dir"), type = "character"), - make_option("--pa", type = "character"), - make_option("--xset", type = "character"), - make_option("--ppm", default = 10), - make_option("--plim", default = 0.0), - make_option("--convert2RawRT", action = "store_true"), - make_option("--intense", action = "store_true"), - make_option("--createDB", action = "store_true"), - make_option("--cores", default = 4), - make_option("--mzML_files", type = "character"), - make_option("--galaxy_names", type = "character"), - make_option("--grp_peaklist", type = "character"), - make_option("--useGroup", action = "store_true") + make_option(c("-o", "--out_dir"), type = "character"), + make_option("--pa", type = "character"), + make_option("--xset", type = "character"), + make_option("--ppm", default = 10), + make_option("--plim", default = 0.0), + make_option("--convert2RawRT", action = "store_true"), + make_option("--intense", action = "store_true"), + make_option("--createDB", action = "store_true"), + make_option("--cores", default = 4), + make_option("--mzML_files", type = "character"), + make_option("--galaxy_names", type = "character"), + make_option("--grp_peaklist", type = "character"), + make_option("--useGroup", action = "store_true") ) # store options @@ -68,17 +65,18 @@ print(opt) loadRData <- function(rdata_path, name) { -#loads an RData file, and returns the named xset object if it is there + # loads an RData file, and returns the named xset object if it is there load(rdata_path) return(get(ls()[ls() %in% name])) } # This function retrieve a xset like object -#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +# @author Gildas Le Corguille lecorguille@sb-roscoff.fr getxcmsSetObject <- function(xobject) { # XCMS 1.x - if (class(xobject) == "xcmsSet") + if (class(xobject) == "xcmsSet") { return(xobject) + } # XCMS 3.x if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object @@ -99,20 +97,20 @@ print(xset@filepaths) if (is.null(opt$intense)) { - intense <- FALSE -}else{ - intense <- TRUE + intense <- FALSE +} else { + intense <- TRUE } if (is.null(opt$convert2RawRT)) { convert2RawRT <- FALSE -}else{ +} else { convert2RawRT <- TRUE } if (is.null(opt$createDB)) { createDB <- FALSE -}else{ +} else { createDB <- TRUE } @@ -121,7 +119,7 @@ pa <- fix[[1]] xset <- fix[[2]] useGroup <- FALSE -}else{ +} else { # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object print("useGroup") fix <- xset_pa_filename_fix(opt, pa) @@ -132,22 +130,24 @@ if (is.null(opt$grp_peaklist)) { grp_peaklist <- NA -}else{ +} else { grp_peaklist <- opt$grp_peaklist } print(useGroup) -pa <- msPurity::frag4feature(pa = pa, - xset = xset, - ppm = opt$ppm, - plim = opt$plim, - intense = intense, - convert2RawRT = convert2RawRT, - db_name = "alldata.sqlite", - out_dir = opt$out_dir, - grp_peaklist = grp_peaklist, - create_db = createDB, - use_group = useGroup) +pa <- msPurity::frag4feature( + pa = pa, + xset = xset, + ppm = opt$ppm, + plim = opt$plim, + intense = intense, + convert2RawRT = convert2RawRT, + db_name = "alldata.sqlite", + out_dir = opt$out_dir, + grp_peaklist = grp_peaklist, + create_db = createDB, + use_group = useGroup +) print(pa) save(pa, file = file.path(opt$out_dir, "frag4feature_output.RData")) |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 macros.xml --- a/macros.xml Tue Feb 08 14:04:07 2022 +0000 +++ b/macros.xml Wed Jun 12 16:08:23 2024 +0000 |
| b |
| @@ -1,14 +1,14 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.16.2</token> - <token name="@GALAXY_TOOL_VERSION@">1</token> + <token name="@GALAXY_TOOL_VERSION@">2</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement> <requirement type="package" version="1.46.0" >bioconductor-camera</requirement> <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement> - <requirement type="package" version="1.16.0" >bioconductor-mspuritydata</requirement> + <requirement type="package" version="1.18.0" >bioconductor-mspuritydata</requirement> <requirement type="package" version="1.6.6">r-optparse</requirement> <requirement type="package" version="1.3.1">r-rpostgres</requirement> <requirement type="package" version="0.10.21">r-rmysql</requirement> |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 purityA.R --- a/purityA.R Tue Feb 08 14:04:07 2022 +0000 +++ b/purityA.R Wed Jun 12 16:08:23 2024 +0000 |
| b |
| @@ -3,20 +3,20 @@ print(sessionInfo()) option_list <- list( - make_option(c("-o", "--out_dir"), type = "character"), - make_option("--mzML_files", type = "character"), - make_option("--galaxy_names", type = "character"), - make_option("--minOffset", type = "numeric"), - make_option("--maxOffset", type = "numeric"), - make_option("--ilim", type = "numeric"), - make_option("--iwNorm", default = "none", type = "character"), - make_option("--exclude_isotopes", action = "store_true"), - make_option("--isotope_matrix", type = "character"), - make_option("--mostIntense", action = "store_true"), - make_option("--plotP", action = "store_true"), - make_option("--nearest", action = "store_true"), - make_option("--cores", default = 4), - make_option("--ppmInterp", default = 7) + make_option(c("-o", "--out_dir"), type = "character"), + make_option("--mzML_files", type = "character"), + make_option("--galaxy_names", type = "character"), + make_option("--minOffset", type = "numeric"), + make_option("--maxOffset", type = "numeric"), + make_option("--ilim", type = "numeric"), + make_option("--iwNorm", default = "none", type = "character"), + make_option("--exclude_isotopes", action = "store_true"), + make_option("--isotope_matrix", type = "character"), + make_option("--mostIntense", action = "store_true"), + make_option("--plotP", action = "store_true"), + make_option("--nearest", action = "store_true"), + make_option("--cores", default = 4), + make_option("--ppmInterp", default = 7) ) opt <- parse_args(OptionParser(option_list = option_list)) @@ -25,23 +25,27 @@ if (opt$iwNorm == "none") { iwNorm <- FALSE iwNormFun <- NULL -}else if (opt$iwNorm == "gauss") { +} else if (opt$iwNorm == "gauss") { iwNorm <- TRUE if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { - print("User has to define offsets if using Gaussian normalisation") - }else{ - iwNormFun <- msPurity::iwNormGauss(minOff = -as.numeric(opt$minOffset), - maxOff = as.numeric(opt$maxOffset)) + print("User has to define offsets if using Gaussian normalisation") + } else { + iwNormFun <- msPurity::iwNormGauss( + minOff = -as.numeric(opt$minOffset), + maxOff = as.numeric(opt$maxOffset) + ) } -}else if (opt$iwNorm == "rcosine") { +} else if (opt$iwNorm == "rcosine") { iwNorm <- TRUE if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { - print("User has to define offsets if using R-cosine normalisation") - }else{ - iwNormFun <- msPurity::iwNormRcosine(minOff = -as.numeric(opt$minOffset), - maxOff = as.numeric(opt$maxOffset)) + print("User has to define offsets if using R-cosine normalisation") + } else { + iwNormFun <- msPurity::iwNormRcosine( + minOff = -as.numeric(opt$minOffset), + maxOff = as.numeric(opt$maxOffset) + ) } -}else if (opt$iwNorm == "QE5") { +} else if (opt$iwNorm == "QE5") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormQE.5() } @@ -53,27 +57,27 @@ if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { offsets <- NA -}else{ +} else { offsets <- as.numeric(c(opt$minOffset, opt$maxOffset)) } if (is.null(opt$mostIntense)) { mostIntense <- FALSE -}else{ +} else { mostIntense <- TRUE } if (is.null(opt$nearest)) { nearest <- FALSE -}else{ +} else { nearest <- TRUE } if (is.null(opt$plotP)) { plotP <- FALSE plotdir <- NULL -}else{ +} else { plotP <- TRUE plotdir <- opt$out_dir } @@ -81,32 +85,34 @@ if (is.null(opt$isotope_matrix)) { im <- NULL -}else{ +} else { im <- read.table(opt$isotope_matrix, - header = TRUE, sep = "\t", stringsAsFactors = FALSE) + header = TRUE, sep = "\t", stringsAsFactors = FALSE + ) } if (is.null(opt$exclude_isotopes)) { isotopes <- FALSE -}else{ +} else { isotopes <- TRUE } pa <- msPurity::purityA(filepaths, - cores = opt$cores, - mostIntense = mostIntense, - nearest = nearest, - offsets = offsets, - plotP = plotP, - plotdir = plotdir, - interpol = "linear", - iwNorm = iwNorm, - iwNormFun = iwNormFun, - ilim = opt$ilim, - mzRback = "pwiz", - isotopes = isotopes, - im = im, - ppmInterp = opt$ppmInterp) + cores = opt$cores, + mostIntense = mostIntense, + nearest = nearest, + offsets = offsets, + plotP = plotP, + plotdir = plotdir, + interpol = "linear", + iwNorm = iwNorm, + iwNormFun = iwNormFun, + ilim = opt$ilim, + mzRback = "pwiz", + isotopes = isotopes, + im = im, + ppmInterp = opt$ppmInterp +) if (!is.null(opt$galaxy_names)) { |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 purityX.R --- a/purityX.R Tue Feb 08 14:04:07 2022 +0000 +++ b/purityX.R Wed Jun 12 16:08:23 2024 +0000 |
| [ |
| @@ -22,7 +22,7 @@ make_option("--galaxy_files", type = "character"), make_option("--choose_class", type = "character"), make_option("--ignore_files", type = "character"), - make_option("--rtraw_columns", action = "store_true") + make_option("--rtraw_columns", action = "store_true") ) @@ -31,9 +31,9 @@ if (!is.null(opt$xgroups)) { - xgroups <- as.numeric(strsplit(opt$xgroups, ",")[[1]]) -}else{ - xgroups <- NULL + xgroups <- as.numeric(strsplit(opt$xgroups, ",")[[1]]) +} else { + xgroups <- NULL } @@ -44,55 +44,75 @@ } if (is.null(opt$isotope_matrix)) { - im <- NULL -}else{ - im <- read.table(opt$isotope_matrix, - header = TRUE, sep = "\t", stringsAsFactors = FALSE) + 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 + isotopes <- FALSE +} else { + isotopes <- TRUE } if (is.null(opt$rtraw_columns)) { - rtraw_columns <- FALSE -}else{ - rtraw_columns <- TRUE + rtraw_columns <- FALSE +} else { + rtraw_columns <- TRUE } loadRData <- function(rdata_path, xset_name) { -#loads an RData file, and returns the named xset object if it is there - load(rdata_path) - return(get(ls()[ls() == xset_name])) + # loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() == xset_name])) +} + + + + +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") { + return(xobject) + } + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, "xcmsSet")) + sampclass(xset) <- xset@phenoData$sample_group + return(xset) + } } target_obj <- loadRData(opt$xset_path, opt$rdata_name) if (opt$camera_xcms == "camera") { - xset <- target_obj@xcmsSet -}else{ - xset <- target_obj + xset <- target_obj@xcmsSet +} else { + xset <- target_obj } +xset <- getxcmsSetObject(xset) + print(xset) minOffset <- as.numeric(opt$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$iwNorm == "QE5") { - iwNorm <- TRUE - iwNormFun <- msPurity::iwNormQE.5() + iwNorm <- FALSE + iwNormFun <- NULL +} else if (opt$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) @@ -105,13 +125,13 @@ 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$galaxy_files)) { + galaxy_files <- trimws(strsplit(opt$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$choose_class)) { @@ -121,7 +141,7 @@ print("choose class") print(ignore_files_class) -}else{ +} else { ignore_files_class <- NA } @@ -132,37 +152,40 @@ ignore_files <- unique(c(ignore_files, ignore_files_class)) ignore_files <- ignore_files[ignore_files != ""] -}else{ +} else { if (anyNA(ignore_files_class)) { ignore_files <- NULL - }else{ + } else { ignore_files <- ignore_files_class } - } print("ignore_files") print(ignore_files) -ppLCMS <- msPurity::purityX(xset = xset, - offsets = c(minOffset, maxOffset), - cores = opt$cores, - xgroups = xgroups, - purityType = opt$purityType, - ilim = opt$ilim, - isotopes = isotopes, - im = im, - iwNorm = iwNorm, - iwNormFun = iwNormFun, - singleFile = opt$singleFile, - fileignore = ignore_files, - rtrawColumns = rtraw_columns) +ppLCMS <- msPurity::purityX( + xset = xset, + offsets = c(minOffset, maxOffset), + cores = opt$cores, + xgroups = xgroups, + purityType = opt$purityType, + ilim = opt$ilim, + isotopes = isotopes, + im = im, + iwNorm = iwNorm, + iwNormFun = iwNormFun, + singleFile = opt$singleFile, + fileignore = ignore_files, + rtrawColumns = rtraw_columns +) dfp <- ppLCMS@predictions # to make compatable with deconrank -colnames(dfp)[colnames(dfp) == "grpid"] <- "peakID" +# (keep grpid for other compatibility) +dfp <- data.frame("peakID"=dfp$grpid, dfp) + colnames(dfp)[colnames(dfp) == "median"] <- "medianPurity" colnames(dfp)[colnames(dfp) == "mean"] <- "meanPurity" colnames(dfp)[colnames(dfp) == "sd"] <- "sdPurity" |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 test-data/combineAnnotations_combined_annotations.sqlite |
| b |
| Binary file test-data/combineAnnotations_combined_annotations.sqlite has changed |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 test-data/combineAnnotations_combined_annotations.tsv --- a/test-data/combineAnnotations_combined_annotations.tsv Tue Feb 08 14:04:07 2022 +0000 +++ b/test-data/combineAnnotations_combined_annotations.tsv Wed Jun 12 16:08:23 2024 +0000 |
| [ |
| b'@@ -1,102 +1,106 @@\n "grpid"\t"grp_name"\t"mz"\t"rt"\t"inchikey"\t"inchi"\t"inchikey"\t"inchikey1"\t"inchikey2"\t"inchikey3"\t"name"\t"exact_mass"\t"molecular_formula"\t"pubchem_cids"\t"kegg_cids"\t"kegg_brite"\t"kegg_drugs"\t"hmdb_ids"\t"hmdb_bio_custom_flag"\t"hmdb_drug_flag"\t"biosim_max_count"\t"biosim_hmdb_ids"\t"fragmentation_acquistion_num"\t"mean_precursor_ion_purity"\t"accession"\t"sirius_score"\t"sirius_wscore"\t"metfrag_score"\t"metfrag_wscore"\t"sm_score"\t"sm_wscore"\t"probmetab_score"\t"probmetab_wscore"\t"ms1_lookup_score"\t"ms1_lookup_wscore"\t"biosim_max_score"\t"biosim_wscore"\t"wscore"\t"rank"\t"adduct_overall"\n 12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-UHFFFAOYSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)"\t"ONIBWKKTOPOVIA-UHFFFAOYSA-N"\t"ONIBWKKTOPOVIA"\t"UHFFFAOYSA"\t"N"\t"DL-Proline"\t115.063328534\t"C5H9NO2"\t"614,25246272"\t"C16435"\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\t"CCMSLIB00000577898"\t"1.0"\t0.2\t0.9\t0.18\t0.87867085623127\t0.263601256869381\t0\t0\t0\t0\t1\t0.25\t0.893601256869381\t1\t"[M+H]+,M+H"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-AZXPZELESA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i4+1"\t"ONIBWKKTOPOVIA-AZXPZELESA-N"\t"ONIBWKKTOPOVIA"\t"AZXPZELESA"\t"N"\t""\t116.066683369\t"C5H9NO2"\t"10290769"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-BYPYZUCNSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"\t"ONIBWKKTOPOVIA-BYPYZUCNSA-N"\t"ONIBWKKTOPOVIA"\t"BYPYZUCNSA"\t"N"\t"L-Pro"\t115.063328534\t"C5H9NO2"\t"145742,6971047"\t"C00148"\t"Compounds with biological roles [BR:br08001]"\t"D00035"\t"HMDB0000162"\t"True"\t"False"\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-GIZBTRSZSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i1+2,2+2,3+2,4+2,5+2"\t"ONIBWKKTOPOVIA-GIZBTRSZSA-N"\t"ONIBWKKTOPOVIA"\t"GIZBTRSZSA"\t"N"\t"L-PROLINE, [U-14C]"\t125.0795385\t"C5H9NO2"\t"12210869"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-GTTLGWSSSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i1+1D,4+1,6+1/t1?,4-"\t"ONIBWKKTOPOVIA-GTTLGWSSSA-N"\t"ONIBWKKTOPOVIA"\t"GTTLGWSSSA"\t"N"\t"SCHEMBL16945363"\t119.07334984\t"C5H9NO2"\t"118264374"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-HOSYLAQJSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i5+1"\t"ONIBWKKTOPOVIA-HOSYLAQJSA-N"\t"ONIBWKKTOPOVIA"\t"HOSYLAQJSA"\t"N"\t"DL-Proline-1-13C"\t116.066683369\t"C5H9NO2"\t"59340910"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-IDEBNGHGSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i1+1,2+1,3+1,4+1,5+1,6+1"\t"ONIBWKKTOPOVIA-IDEBNGHGSA-N"\t"ONIBWKKTOPOVIA"\t"IDEBNGHGSA"\t"N"\t"SCHEMBL18875607"\t121.0771376\t"C5H9NO2"\t"129148531"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-IXBOUXNVSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i4+1"\t"ONIBWKKTOPOVIA-IXBOUXNVSA-N"\t"ONIBWKKTOPOVIA"\t"IXBOUXNVSA"\t"N"\t""\t116.066683369\t"C5H9NO2"\t"100915807"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-JGTYJTGKSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i6+1"\t"ONIBWKKTOPOVIA-JGTYJTGKSA-N"\t"ONIBWKKTOPOVIA"\t"JGTYJTGKSA"\t"N"\t"L-Proline-15N"\t116.06036343\t"C5H9NO2"\t'..b'/i3D2,4D2"\t"RWRDLPDLKQPQOW-KHORGVISSA-N"\t"RWRDLPDLKQPQOW"\t"KHORGVISSA"\t"N"\t"ACM42403258"\t75.098606278\t"C4H9N"\t"12196049"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t16\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-MNYXATJNSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i/hT"\t"RWRDLPDLKQPQOW-MNYXATJNSA-N"\t"RWRDLPDLKQPQOW"\t"MNYXATJNSA"\t"N"\t""\t73.081723544\t"C4H9N"\t"57750053"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t16\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-SMZGMGDZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i3D2"\t"RWRDLPDLKQPQOW-SMZGMGDZSA-N"\t"RWRDLPDLKQPQOW"\t"SMZGMGDZSA"\t"N"\t""\t73.086052786\t"C4H9N"\t"57608710"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t16\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-LNLMKGTHSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2"\t"RWRDLPDLKQPQOW-LNLMKGTHSA-N"\t"RWRDLPDLKQPQOW"\t"LNLMKGTHSA"\t"N"\t""\t75.098606278\t"C4H9N"\t"57608709"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8333\t0.208325\t0.208325\t17\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-QAOQSSEZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D,3D2"\t"RWRDLPDLKQPQOW-QAOQSSEZSA-N"\t"RWRDLPDLKQPQOW"\t"QAOQSSEZSA"\t"N"\t""\t74.092329532\t"C4H9N"\t"90927493"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8\t0.2\t0.2\t18\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-SVYQBANQSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D2,4D2"\t"RWRDLPDLKQPQOW-SVYQBANQSA-N"\t"RWRDLPDLKQPQOW"\t"SVYQBANQSA"\t"N"\t"Pyrrolidine-2,2,3,3,4,4,5,5-d8"\t79.123713262\t"C4H9N"\t"12196044"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8\t0.2\t0.2\t18\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-HJOWPTDZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D,4D2/hD"\t"RWRDLPDLKQPQOW-HJOWPTDZSA-N"\t"RWRDLPDLKQPQOW"\t"HJOWPTDZSA"\t"N"\t"pyrrolidine-d8"\t79.123713262\t"C4H9N"\t"129715569"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.7143\t0.178575\t0.178575\t19\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-KLRAWXKOSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D2,4D2/hD"\t"RWRDLPDLKQPQOW-KLRAWXKOSA-N"\t"RWRDLPDLKQPQOW"\t"KLRAWXKOSA"\t"N"\t""\t80.12999001\t"C4H9N"\t"60135501"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.7143\t0.178575\t0.178575\t19\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"MWFMGBPGAXYFAR-UHFFFAOYSA-N"\t"InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3"\t"MWFMGBPGAXYFAR-UHFFFAOYSA-N"\t"MWFMGBPGAXYFAR"\t"UHFFFAOYSA"\t"N"\t"ACETONE CYANOHYDRIN"\t85.05276385\t"C4H7NO"\t"6406"\t"C02659"\t""\t""\t"HMDB0060427"\t"False"\t"False"\t0\t"HMDB0031456"\t"277,343,409,410"\t0.99\tNA\t"0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.6923\t0.173075\t0.173075\t20\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RRUDCFGSUDOHDG-UHFFFAOYSA-N"\t"InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4)"\t"RRUDCFGSUDOHDG-UHFFFAOYSA-N"\t"RRUDCFGSUDOHDG"\t"UHFFFAOYSA"\t"N"\t"acetohydroxamic acid"\t75.032028405\t"C2H5NO2"\t"1990"\t"C06808"\t"Anatomical Therapeutic Chemical (ATC) classification [BR:br08303]"\t"D00220"\t"HMDB0014691"\t"False"\t"True"\t0\t"HMDB0003338"\t"277,343,409,410"\t0.99\tNA\t"0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.5455\t0.136375\t0.136375\t21\t"[M+H]+"\n 27\t"M132T74"\t132.101827517612\t73.554846736017\t"AGPKZVBTJJNPAG-UHFFFAOYSA-N"\t"InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)"\t"AGPKZVBTJJNPAG-UHFFFAOYSA-N"\t"AGPKZVBTJJNPAG"\t"UHFFFAOYSA"\t"N"\t"2-ammonio-3-methylpentanoate"\t131.09462866\t"C6H13NO2"\t"791,57397079"\t"C16434"\t""\t""\t"HMDB0033923"\t"True"\t"False"\t18\t"HMDB0000172"\t"478,547,616,475,541,607"\t1\t"CE000616"\t"0"\t0\t0\t0\t0.940890528192141\t0.282267158457642\t0\t0\t0\t0\t1\t0.25\t0.532267158457642\t1\t"[M+H]+"\n' |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 test-data/purityX_output.RData |
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| Binary file test-data/purityX_output.RData has changed |
| b |
| diff -r e9fbb65451f6 -r cb4aeec93d49 test-data/purityX_output.tsv --- a/test-data/purityX_output.tsv Tue Feb 08 14:04:07 2022 +0000 +++ b/test-data/purityX_output.tsv Wed Jun 12 16:08:23 2024 +0000 |
| b |
| @@ -0,0 +1,16 @@ +"peakID" "grpid" "meanPurity" "medianPurity" "sdPurity" "sdePurity" "cvPurity" "pknmPurity" "i" "mz" +1 1 1 1 0 0 0 1 61925043.3566382 102.091560881174 +2 2 1 1 0 0 0 1 25719001.4822415 103.054435681307 +3 3 1 1 0 0 0 1 3791623.64689146 103.094714179046 +4 4 1 1 0 0 0 1 701844279.87476 104.107044269271 +5 5 0.753862395887935 1 0.49227520822413 0.246137604112065 65.3004064016622 1 79111202.7215235 105.051698129502 +6 6 0.849777173964078 0.846538530688927 0.0251183222605269 0.0125591611302635 2.95587161318465 2 5735625.74118929 106.062931911485 +7 7 0.846273037079121 0.84212559075998 0.0578505242577427 0.0289252621288714 6.83591721856241 2.25 2124533.28227443 107.050950030548 +8 8 1 1 0 0 0 1 1965138.01789635 108.006429726299 +9 9 1 1 0 0 0 1 362848.770317471 108.055140508271 +10 10 1 1 0 0 0 1 25053032.2987587 110.071444659587 +11 11 0.657159557553984 0.66469615675609 0.396069303079897 0.198034651539948 60.269884007182 3 8168571.28564153 111.020205687498 +12 12 0.986752431352875 0.987973697141727 0.0154264299310987 0.00771321496554933 1.56335362761138 1.25 21655562.9118763 112.043935634745 +13 13 0.969931320369093 0.973488648484343 0.035202929071034 0.017601464535517 3.6294249223376 1.5 16160213.3493717 112.923083776231 +14 14 1 1 0 0 0 1 82880594.6142923 113.035283604395 +15 15 0.613847507731082 0.613847507731082 0.00533923101597845 0.0037754064577199 0.869797620538273 4 3386134.01927015 114.037770729384 |