Expose 'addAbundanceValues' argument to include or exclude abundance values in result tables

Author: csoneson

NEWS.md

@@ -1,3 +1,7 @@
+# einprot 0.9.8
+
+* Expose argument to include or exclude abundance values from result tables
+
 # einprot 0.9.7
 
 * Adapt to (and require) msigdbr >= v10.0.0

R/checkArgumentsDIANN.R

@@ -10,8 +10,8 @@
     forceOverwrite, experimentInfo, species, diannFile, diannFileType,
     outLevel, diannLogFile, aName, idCol, labelCol, geneIdCol, proteinIdCol,
     stringIdCol, extraFeatureCols, sampleAnnot, includeOnlySamples,
-    excludeSamples, minScore,
-    minPeptides, imputeMethod, assaysForExport, addHeatmaps, mergeGroups,
+    excludeSamples, minScore, minPeptides, imputeMethod, assaysForExport, 
+    addAbundanceValues, addHeatmaps, mergeGroups,
     comparisons, ctrlGroup, allPairwiseComparisons, singleFit,
     subtractBaseline, baselineGroup, normMethod, spikeFeatures, stattest,
     minNbrValidValues, minlFC, samSignificance, nperm, volcanoAdjPvalThr,
@@ -143,6 +143,7 @@
     .assertScalar(x = imputeMethod, type = "character",
                   validValues = c("impSeqRob", "MinProb", "MinProbGlobal"))
     .assertVector(x = assaysForExport, type = "character", allowNULL = TRUE)
+    .assertScalar(x = addAbundanceValues, type = "logical")
     .assertScalar(x = addHeatmaps, type = "logical")
     .assertScalar(x = normMethod, type = "character",
                   validValues = c(MsCoreUtils::normalizeMethods(), "none",

R/checkArgumentsFragPipe.R

@@ -10,7 +10,8 @@
     forceOverwrite, experimentInfo, species, fragpipeDir,
     idCol, labelCol, geneIdCol, proteinIdCol, stringIdCol, extraFeatureCols,
     iColPattern, sampleAnnot, includeOnlySamples, excludeSamples, minScore,
-    minPeptides, imputeMethod, assaysForExport, addHeatmaps, mergeGroups,
+    minPeptides, imputeMethod, assaysForExport, addAbundanceValues, 
+    addHeatmaps, mergeGroups,
     comparisons, ctrlGroup, allPairwiseComparisons, singleFit,
     subtractBaseline, baselineGroup, normMethod, spikeFeatures, stattest,
     minNbrValidValues, minlFC, samSignificance, nperm, volcanoAdjPvalThr,
@@ -148,6 +149,7 @@
     .assertScalar(x = imputeMethod, type = "character",
                   validValues = c("impSeqRob", "MinProb", "MinProbGlobal"))
     .assertVector(x = assaysForExport, type = "character", allowNULL = TRUE)
+    .assertScalar(x = addAbundanceValues, type = "logical")
     .assertScalar(x = addHeatmaps, type = "logical")
     .assertScalar(x = normMethod, type = "character",
                   validValues = c(MsCoreUtils::normalizeMethods(), "none",

R/checkArgumentsMaxQuant.R

@@ -10,7 +10,8 @@
     forceOverwrite, experimentInfo, species, mqFile, mqParameterFile,
     idCol, labelCol, geneIdCol, proteinIdCol, stringIdCol, extraFeatureCols,
     iColPattern, sampleAnnot, includeOnlySamples, excludeSamples, minScore,
-    minPeptides, imputeMethod, assaysForExport, addHeatmaps, mergeGroups,
+    minPeptides, imputeMethod, assaysForExport, addAbundanceValues, 
+    addHeatmaps, mergeGroups,
     comparisons, ctrlGroup, allPairwiseComparisons, singleFit,
     subtractBaseline, baselineGroup, normMethod, spikeFeatures, stattest,
     minNbrValidValues, minlFC, samSignificance, nperm, volcanoAdjPvalThr,
@@ -133,6 +134,7 @@
     .assertScalar(x = imputeMethod, type = "character",
                   validValues = c("impSeqRob", "MinProb", "MinProbGlobal"))
     .assertVector(x = assaysForExport, type = "character", allowNULL = TRUE)
+    .assertScalar(x = addAbundanceValues, type = "logical")
     .assertScalar(x = addHeatmaps, type = "logical")
     .assertScalar(x = normMethod, type = "character",
                   validValues = c(MsCoreUtils::normalizeMethods(), "none",

R/checkArgumentsPDTMT.R

@@ -13,7 +13,7 @@
     modificationsCol, excludeUnmodifiedPeptides, keepModifications,
     iColPattern, sampleAnnot, includeOnlySamples, excludeSamples,
     minScore, minDeltaScore, minPeptides, minPSMs, masterProteinsOnly,
-    imputeMethod, assaysForExport, addHeatmaps, mergeGroups,
+    imputeMethod, assaysForExport, addAbundanceValues, addHeatmaps, mergeGroups,
     comparisons, ctrlGroup, allPairwiseComparisons, singleFit,
     subtractBaseline, baselineGroup, normMethod, spikeFeatures, stattest,
     minNbrValidValues, minlFC, samSignificance, nperm, volcanoAdjPvalThr,
@@ -156,6 +156,7 @@
     .assertScalar(x = imputeMethod, type = "character",
                   validValues = c("impSeqRob", "MinProb", "MinProbGlobal"))
     .assertVector(x = assaysForExport, type = "character", allowNULL = TRUE)
+    .assertScalar(x = addAbundanceValues, type = "logical")
     .assertScalar(x = addHeatmaps, type = "logical")
     .assertScalar(x = normMethod, type = "character",
                   validValues = c(MsCoreUtils::normalizeMethods(), "none",

R/checkArgumentsSpectronaut.R

@@ -11,8 +11,8 @@
     spectronautFileType, outLevel,
     spectronautLogFile, aName, idCol, labelCol, geneIdCol, proteinIdCol,
     stringIdCol, extraFeatureCols, iColPattern, sampleAnnot, includeOnlySamples,
-    excludeSamples, minScore,
-    minPeptides, imputeMethod, assaysForExport, addHeatmaps, mergeGroups,
+    excludeSamples, minScore, minPeptides, imputeMethod, assaysForExport, 
+    addAbundanceValues, addHeatmaps, mergeGroups,
     comparisons, ctrlGroup, allPairwiseComparisons, singleFit,
     subtractBaseline, baselineGroup, normMethod, spikeFeatures, stattest,
     minNbrValidValues, minlFC, samSignificance, nperm, volcanoAdjPvalThr,
@@ -146,6 +146,7 @@
     .assertScalar(x = imputeMethod, type = "character",
                   validValues = c("impSeqRob", "MinProb", "MinProbGlobal"))
     .assertVector(x = assaysForExport, type = "character", allowNULL = TRUE)
+    .assertScalar(x = addAbundanceValues, type = "logical")
     .assertScalar(x = addHeatmaps, type = "logical")
     .assertScalar(x = normMethod, type = "character",
                   validValues = c(MsCoreUtils::normalizeMethods(), "none",

R/runDIANNAnalysis.R

@@ -133,8 +133,8 @@ runDIANNAnalysis <- function(
     sampleAnnot,
     includeOnlySamples = "", excludeSamples = "",
     minScore = 10, minPeptides = 2, imputeMethod = "MinProb",
-    assaysForExport = NULL, addHeatmaps = TRUE, mergeGroups = list(),
-    comparisons = list(),
+    assaysForExport = NULL, addAbundanceValues = TRUE, 
+    addHeatmaps = TRUE, mergeGroups = list(), comparisons = list(),
     ctrlGroup = "", allPairwiseComparisons = TRUE, singleFit = TRUE,
     subtractBaseline = FALSE, baselineGroup = "", normMethod = "none",
     spikeFeatures = NULL, stattest = "limma", minNbrValidValues = 2,
@@ -183,7 +183,8 @@ runDIANNAnalysis <- function(
         includeOnlySamples = includeOnlySamples,
         excludeSamples = excludeSamples, minScore = minScore,
         minPeptides = minPeptides, imputeMethod = imputeMethod,
-        assaysForExport = assaysForExport, addHeatmaps = addHeatmaps,
+        assaysForExport = assaysForExport, 
+        addAbundanceValues = addAbundanceValues, addHeatmaps = addHeatmaps,
         mergeGroups = mergeGroups,
         comparisons = comparisons, ctrlGroup = ctrlGroup,
         allPairwiseComparisons = allPairwiseComparisons, singleFit = singleFit,
@@ -237,8 +238,9 @@ runDIANNAnalysis <- function(
              includeOnlySamples = includeOnlySamples,
              excludeSamples = excludeSamples, minScore = minScore,
              minPeptides = minPeptides, imputeMethod = imputeMethod,
-             assaysForExport = assaysForExport, addHeatmaps = addHeatmaps,
-             mergeGroups = mergeGroups,
+             assaysForExport = assaysForExport, 
+             addAbundanceValues = addAbundanceValues, 
+             addHeatmaps = addHeatmaps, mergeGroups = mergeGroups,
              comparisons = comparisons, ctrlGroup = ctrlGroup,
              allPairwiseComparisons = allPairwiseComparisons,
              singleFit = singleFit,

R/runFragPipeAnalysis.R

@@ -84,8 +84,8 @@ runFragPipeAnalysis <- function(
     iColPattern, sampleAnnot,
     includeOnlySamples = "", excludeSamples = "",
     minScore = 10, minPeptides = 2, imputeMethod = "MinProb",
-    assaysForExport = NULL, addHeatmaps = TRUE, mergeGroups = list(),
-    comparisons = list(),
+    assaysForExport = NULL, addAbundanceValues = TRUE, 
+    addHeatmaps = TRUE, mergeGroups = list(), comparisons = list(),
     ctrlGroup = "", allPairwiseComparisons = TRUE, singleFit = TRUE,
     subtractBaseline = FALSE, baselineGroup = "", normMethod = "none",
     spikeFeatures = NULL, stattest = "limma", minNbrValidValues = 2,
@@ -133,7 +133,8 @@ runFragPipeAnalysis <- function(
         sampleAnnot = sampleAnnot, includeOnlySamples = includeOnlySamples,
         excludeSamples = excludeSamples, minScore = minScore,
         minPeptides = minPeptides, imputeMethod = imputeMethod,
-        assaysForExport = assaysForExport, addHeatmaps = addHeatmaps,
+        assaysForExport = assaysForExport, 
+        addAbundanceValues = addAbundanceValues, addHeatmaps = addHeatmaps,
         mergeGroups = mergeGroups,
         comparisons = comparisons, ctrlGroup = ctrlGroup,
         allPairwiseComparisons = allPairwiseComparisons, singleFit = singleFit,
@@ -184,7 +185,8 @@ runFragPipeAnalysis <- function(
              sampleAnnot = sampleAnnot, includeOnlySamples = includeOnlySamples,
              excludeSamples = excludeSamples, minScore = minScore,
              minPeptides = minPeptides, imputeMethod = imputeMethod,
-             assaysForExport = assaysForExport, addHeatmaps = addHeatmaps,
+             assaysForExport = assaysForExport, 
+             addAbundanceValues = addAbundanceValues, addHeatmaps = addHeatmaps,
              mergeGroups = mergeGroups,
              comparisons = comparisons, ctrlGroup = ctrlGroup,
              allPairwiseComparisons = allPairwiseComparisons,

R/runMaxQuantAnalysis.R

@@ -80,6 +80,8 @@
 #'     if another assay is used for the actual analysis and comparison of
 #'     groups. If set to \code{NULL} or an assay name that does not exist in
 #'     the SingleCellExperiment object, the 'main' assay will be used.
+#' @param addAbundanceValues Logical scalar defining whether abundance values
+#'     for individual samples should be added to the exported result tables.  
 #' @param addHeatmaps Logical scalar indicating whether to include heatmaps
 #'     or not. This controls both the heatmap showing the missing value
 #'     pattern in the data, as well as the summary heatmaps of the
@@ -269,7 +271,8 @@ runMaxQuantAnalysis <- function(
     iColPattern, sampleAnnot,
     includeOnlySamples = "", excludeSamples = "",
     minScore = 10, minPeptides = 2, imputeMethod = "MinProb",
-    assaysForExport = c("iBAQ", "Top3"), addHeatmaps = TRUE,
+    assaysForExport = c("iBAQ", "Top3"), 
+    addAbundanceValues = TRUE, addHeatmaps = TRUE,
     mergeGroups = list(), comparisons = list(),
     ctrlGroup = "", allPairwiseComparisons = TRUE, singleFit = TRUE,
     subtractBaseline = FALSE, baselineGroup = "", normMethod = "none",
@@ -319,7 +322,8 @@ runMaxQuantAnalysis <- function(
         includeOnlySamples = includeOnlySamples,
         excludeSamples = excludeSamples, minScore = minScore,
         minPeptides = minPeptides, imputeMethod = imputeMethod,
-        assaysForExport = assaysForExport, addHeatmaps = addHeatmaps,
+        assaysForExport = assaysForExport, 
+        addAbundanceValues = addAbundanceValues, addHeatmaps = addHeatmaps,
         mergeGroups = mergeGroups,
         comparisons = comparisons, ctrlGroup = ctrlGroup,
         allPairwiseComparisons = allPairwiseComparisons, singleFit = singleFit,
@@ -372,8 +376,9 @@ runMaxQuantAnalysis <- function(
              includeOnlySamples = includeOnlySamples,
              excludeSamples = excludeSamples, minScore = minScore,
              minPeptides = minPeptides, imputeMethod = imputeMethod,
-             assaysForExport = assaysForExport, addHeatmaps = addHeatmaps,
-             mergeGroups = mergeGroups,
+             assaysForExport = assaysForExport, 
+             addAbundanceValues = addAbundanceValues, 
+             addHeatmaps = addHeatmaps, mergeGroups = mergeGroups,
              comparisons = comparisons, ctrlGroup = ctrlGroup,
              allPairwiseComparisons = allPairwiseComparisons,
              singleFit = singleFit,

R/runPDTMTAnalysis.R

@@ -131,8 +131,8 @@ runPDTMTAnalysis <- function(
     includeOnlySamples = "", excludeSamples = "",
     minScore = 2, minDeltaScore = 0.2, minPeptides = 2, minPSMs = 2,
     masterProteinsOnly = FALSE, imputeMethod = "MinProb",
-    assaysForExport = NULL, addHeatmaps = TRUE, mergeGroups = list(),
-    comparisons = list(),
+    assaysForExport = NULL, addAbundanceValues = TRUE, 
+    addHeatmaps = TRUE, mergeGroups = list(), comparisons = list(),
     ctrlGroup = "", allPairwiseComparisons = TRUE, singleFit = TRUE,
     subtractBaseline = FALSE, baselineGroup = "", normMethod = "none",
     spikeFeatures = NULL, stattest = "limma", minNbrValidValues = 2,
@@ -189,7 +189,7 @@ runPDTMTAnalysis <- function(
         minPeptides = minPeptides, minPSMs = minPSMs,
         masterProteinsOnly = masterProteinsOnly,
         imputeMethod = imputeMethod, assaysForExport = assaysForExport,
-        addHeatmaps = addHeatmaps,
+        addAbundanceValues = addAbundanceValues, addHeatmaps = addHeatmaps,
         mergeGroups = mergeGroups, comparisons = comparisons,
         ctrlGroup = ctrlGroup, allPairwiseComparisons = allPairwiseComparisons,
         singleFit = singleFit,
@@ -249,7 +249,7 @@ runPDTMTAnalysis <- function(
              minPeptides = minPeptides, minPSMs = minPSMs,
              masterProteinsOnly = masterProteinsOnly,
              imputeMethod = imputeMethod, assaysForExport = assaysForExport,
-             addHeatmaps = addHeatmaps,
+             addAbundanceValues = addAbundanceValues, addHeatmaps = addHeatmaps,
              mergeGroups = mergeGroups, comparisons = comparisons,
              ctrlGroup = ctrlGroup,
              allPairwiseComparisons = allPairwiseComparisons,