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Merge pull request #5 from fmicompbio/add-fragpipe
Add FragPipe
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| Package: einprot | ||
| Type: Package | ||
| Title: A collection of proteomics analysis utilities and workflows | ||
| Version: 0.6.5 | ||
| Version: 0.6.8 | ||
| Authors@R: c( | ||
| person("Charlotte", "Soneson", email = "[email protected]", | ||
| role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3833-2169")), | ||
|
|
@@ -74,6 +74,7 @@ RoxygenNote: 7.2.3 | |
| Suggests: | ||
| BiocManager, | ||
| testthat (>= 3.0.0), | ||
| iSEE | ||
| iSEE, | ||
| matrixStats | ||
| Config/testthat/edition: 3 | ||
| VignetteBuilder: knitr | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,201 @@ | ||
| #' Check validity of arguments for FragPipe analysis | ||
| #' | ||
| #' @keywords internal | ||
| #' @noRd | ||
| #' @author Charlotte Soneson | ||
| #' | ||
| #' @importFrom MsCoreUtils normalizeMethods | ||
| .checkArgumentsFragPipe <- function( | ||
| templateRmd, outputDir, outputBaseName, reportTitle, reportAuthor, | ||
| forceOverwrite, experimentInfo, species, fragpipeDir, | ||
| idCol, labelCol, geneIdCol, proteinIdCol, stringIdCol, | ||
| iColPattern, sampleAnnot, includeOnlySamples, | ||
| excludeSamples, minScore, minPeptides, imputeMethod, mergeGroups, | ||
| comparisons, ctrlGroup, allPairwiseComparisons, singleFit, | ||
| subtractBaseline, baselineGroup, normMethod, spikeFeatures, stattest, | ||
| minNbrValidValues, minlFC, samSignificance, nperm, volcanoAdjPvalThr, | ||
| volcanoLog2FCThr, volcanoMaxFeatures, volcanoS0, volcanoFeaturesToLabel, | ||
| addInteractiveVolcanos, interactiveDisplayColumns, complexFDRThr, | ||
| maxNbrComplexesToPlot, seed, | ||
| includeFeatureCollections, minSizeToKeepSet, customComplexes, | ||
| complexSpecies, complexDbPath, stringVersion, stringDir, linkTableColumns, | ||
| customYml, doRender | ||
| ) { | ||
| ## templateRmd | ||
| .assertScalar(x = templateRmd, type = "character") | ||
| if (!file.exists(templateRmd)) { | ||
| stop("'templateRmd' must point to an existing file") | ||
| } | ||
|
|
||
| ## Output specifications | ||
| .assertScalar(x = outputDir, type = "character") | ||
| .assertScalar(x = outputBaseName, type = "character") | ||
| .assertScalar(x = reportTitle, type = "character") | ||
| .assertScalar(x = reportAuthor, type = "character") | ||
| .assertScalar(x = forceOverwrite, type = "logical") | ||
| .assertScalar(x = doRender, type = "logical") | ||
|
|
||
| ## Experiment info | ||
| .assertVector(x = experimentInfo, type = "list") | ||
| if (length(experimentInfo) > 0) { | ||
| .assertVector(x = names(experimentInfo), type = "character") | ||
| } | ||
| tmp <- getSpeciesInfo(species) ## gives an error for unsupported species | ||
|
|
||
| ## FP files | ||
| .assertScalar(x = fragpipeDir, type = "character") | ||
| if (!file.exists(file.path(fragpipeDir, "combined_protein.tsv"))) { | ||
| stop("The file ", | ||
| file.path(fragpipeDir, "combined_protein.tsv"), | ||
| " doesn't exist") | ||
| } | ||
| fpConfigFile <- list.files(fragpipeDir, pattern = "^fragpipe.+.config$", | ||
| full.names = TRUE) | ||
| if (length(fpConfigFile) > 1) { | ||
| stop("There are more than one config file in the FragPipe directory") | ||
| } | ||
| fpLogFile <- list.files(fragpipeDir, pattern = "^log_.+.txt$", | ||
| full.names = TRUE) | ||
| if (length(fpLogFile) > 1) { | ||
| stop("There are more than one log file in the FragPipe directory") | ||
| } | ||
|
|
||
| ## Samples to include or exclude | ||
| .assertVector(x = includeOnlySamples, type = "character") | ||
| .assertVector(x = excludeSamples, type = "character") | ||
| if ((length(includeOnlySamples) > 1 || includeOnlySamples != "") && | ||
| (length(excludeSamples) > 1 || excludeSamples != "")) { | ||
| stop("Please specify max one of includeOnlySamples and excludeSamples") | ||
| } | ||
|
|
||
| ## Names and patterns | ||
| validPatterns <- c("\\\\.Unique\\\\.Spectral\\\\.Count$", | ||
| "\\\\.Total\\\\.Spectral\\\\.Count$", | ||
| "\\\\.Unique\\\\.Intensity$", | ||
| "\\\\.MaxLFQ\\\\.Unique\\\\.Intensity$", | ||
| "\\\\.MaxLFQ\\\\.Total\\\\.Intensity$", | ||
| "\\\\.MaxLFQ\\\\.Intensity$") | ||
| .assertScalar(x = iColPattern, type = "character", | ||
| validValues = c(validPatterns, | ||
| gsub("\\\\", "", validPatterns, fixed = TRUE))) | ||
| .assertVector(x = sampleAnnot, type = "data.frame") | ||
| .assertVector(x = colnames(sampleAnnot), type = "character") | ||
| stopifnot(all(c("sample", "group") %in% colnames(sampleAnnot))) | ||
| .assertVector(x = sampleAnnot$group, type = "character") | ||
| ics <- getIntensityColumns(inFile = file.path(fragpipeDir, | ||
| "combined_protein.tsv"), | ||
| iColPattern = gsub("\\\\", "\\", iColPattern, | ||
| fixed = TRUE), | ||
| includeOnlySamples = includeOnlySamples, | ||
| excludeSamples = excludeSamples, | ||
| stopIfEmpty = TRUE) | ||
| ics <- gsub(gsub("\\\\", "\\", iColPattern, | ||
| fixed = TRUE), "", ics$iCols) | ||
| msg <- setdiff(ics, sampleAnnot$sample) | ||
| if (length(msg) > 0) { | ||
| stop("Not all sample names are available in the sample annotation. ", | ||
| "Missing samples: ", paste(msg, collapse = ",")) | ||
| } | ||
|
|
||
| if (is(idCol, "function")) { | ||
| stopifnot(length(formals(idCol)) == 1) | ||
| } else { | ||
| .assertVector(x = idCol, type = "character") | ||
| } | ||
| if (is(labelCol, "function")) { | ||
| stopifnot(length(formals(labelCol)) == 1) | ||
| } else { | ||
| .assertVector(x = labelCol, type = "character") | ||
| } | ||
| if (is(geneIdCol, "function")) { | ||
| stopifnot(length(formals(geneIdCol)) == 1) | ||
| } else { | ||
| .assertVector(x = geneIdCol, type = "character", allowNULL = TRUE) | ||
| } | ||
| if (is(proteinIdCol, "function")) { | ||
| stopifnot(length(formals(proteinIdCol)) == 1) | ||
| } else { | ||
| .assertVector(x = proteinIdCol, type = "character") | ||
| } | ||
| if (is(stringIdCol, "function")) { | ||
| stopifnot(length(formals(stringIdCol)) == 1) | ||
| } else { | ||
| .assertVector(x = stringIdCol, type = "character", allowNULL = TRUE) | ||
| } | ||
|
|
||
| .assertVector(x = linkTableColumns, type = "character", allowNULL = TRUE) | ||
|
|
||
| ## Score thresholds | ||
| .assertScalar(x = minScore, type = "numeric") | ||
| .assertScalar(x = minPeptides, type = "numeric") | ||
|
|
||
| ## Method choices | ||
| .assertScalar(x = imputeMethod, type = "character", | ||
| validValues = c("impSeqRob", "MinProb")) | ||
| .assertScalar(x = normMethod, type = "character", | ||
| validValues = c(MsCoreUtils::normalizeMethods(), "none")) | ||
| .assertVector(x = spikeFeatures, type = "character", allowNULL = TRUE) | ||
| .assertScalar(x = stattest, type = "character", | ||
| validValues = c("limma", "ttest", "proDA", "none")) | ||
|
|
||
| ## Test parameters | ||
| .assertScalar(x = minNbrValidValues, type = "numeric", rngIncl = c(0, Inf)) | ||
| .assertScalar(x = minlFC, type = "numeric", rngIncl = c(0, Inf)) | ||
| .assertScalar(x = samSignificance, type = "logical") | ||
| .assertScalar(x = nperm, type = "numeric", rngIncl = c(1, Inf)) | ||
| .assertScalar(x = volcanoAdjPvalThr, type = "numeric", rngIncl = c(0, 1)) | ||
| .assertScalar(x = volcanoLog2FCThr, type = "numeric", rngIncl = c(0, Inf)) | ||
| .assertScalar(x = volcanoMaxFeatures, type = "numeric", rngIncl = c(0, Inf)) | ||
| .assertScalar(x = volcanoS0, type = "numeric", rngIncl = c(0, Inf)) | ||
| .assertScalar(x = complexFDRThr, type = "numeric", rngIncl = c(0, 1)) | ||
| .assertScalar(x = maxNbrComplexesToPlot, type = "numeric", rngIncl = c(0, Inf)) | ||
| .assertScalar(x = minSizeToKeepSet, type = "numeric", rngIncl = c(0, Inf)) | ||
| .assertVector(x = volcanoFeaturesToLabel, type = "character") | ||
| .assertVector(x = mergeGroups, type = "list") | ||
| .assertVector(x = comparisons, type = "list") | ||
| .assertScalar(x = ctrlGroup, type = "character") | ||
| .assertScalar(x = allPairwiseComparisons, type = "logical") | ||
| .assertScalar(x = addInteractiveVolcanos, type = "logical") | ||
| .assertVector(x = interactiveDisplayColumns, type = "character", allowNULL = TRUE) | ||
| .assertScalar(x = singleFit, type = "logical") | ||
| .assertScalar(x = subtractBaseline, type = "logical") | ||
| .assertScalar(x = baselineGroup, type = "character") | ||
|
|
||
| if (length(mergeGroups) > 0) { | ||
| if (is.null(names(mergeGroups)) || any(names(mergeGroups) == "") || | ||
| any(duplicated(names(mergeGroups)))) { | ||
| stop("'mergeGroups' must be a named list, without duplicated names") | ||
| } | ||
| } | ||
|
|
||
| if (length(comparisons) > 0) { | ||
| if (!all(vapply(comparisons, length, 0) == 2)) { | ||
| stop("Each entry in 'comparisons' must have exactly two elements") | ||
| } | ||
| } | ||
|
|
||
| ## seed | ||
| .assertScalar(x = seed, type = "numeric", rngIncl = c(1, Inf)) | ||
|
|
||
| ## Complexes | ||
| .assertVector(x = includeFeatureCollections, type = "character", | ||
| validValues = c("complexes", "GO"), allowNULL = TRUE) | ||
| .assertVector(x = customComplexes, type = "list") | ||
| if (length(customComplexes) > 0) { | ||
| .assertVector(x = names(customComplexes), type = "character") | ||
| } | ||
| .assertScalar(x = complexSpecies, type = "character", | ||
| validValues = c("current", "all"), allowNULL = TRUE) | ||
| .assertScalar(x = complexDbPath, type = "character", allowNULL = TRUE) | ||
| if (!is.null(complexDbPath) && !file.exists(complexDbPath)) { | ||
| stop("'complexDbPath' must point to an existing file") | ||
| } | ||
|
|
||
| .assertScalar(x = stringVersion, type = "character") | ||
| .assertScalar(x = stringDir, type = "character", allowNULL = TRUE) | ||
|
|
||
| .assertScalar(x = customYml, type = "character", allowNULL = TRUE) | ||
| if (!is.null(customYml) && !file.exists(customYml)) { | ||
| stop("'customYml' must point to an existing file") | ||
| } | ||
| } |
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