Merge pull request #754 from joshua-d-campbell/devel

Devel
compbiomed · Apr 16, 2024 · a78fbac · a78fbac
2 parents 8e5ee1b + b1f14b6
commit a78fbac
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diff --git a/R/runDEAnalysis.R b/R/runDEAnalysis.R
@@ -266,7 +266,7 @@
 runDEAnalysis <- function(inSCE, method = 'wilcox', ...){
   validMethods <- c('wilcox', 'MAST', 'DESeq2', 'Limma', 'ANOVA')
   method <- match.arg(method, choices = validMethods)
-  funcList <- list(wilcox = function(inSCE, ...) runWilcox(inSCE, classGroup1 = NULL, classGroup2 =NULL, class = NULL, ...), 
+  funcList <- list(wilcox = runWilcox, 
                    MAST = runMAST,
                    DESeq2 = runDESeq2,
                    Limma = runLimmaDE,

diff --git a/R/runFindMarker.R b/R/runFindMarker.R
@@ -93,6 +93,9 @@ runFindMarker <- function(inSCE, useAssay = 'logcounts',
                            useAssay = useAssay,
                            useReducedDim = useReducedDim,
                            index1 = clusterIndex,
+                           class = NULL,
+                           classGroup1 = NULL,
+                           classGroup2 = NULL,
                            analysisName = paste0('findMarker', c),
                            onlyPos = TRUE,
                            log2fcThreshold = log2fcThreshold,

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/01_import_and_qc_tutorial.html b/docs/articles/01_import_and_qc_tutorial.html
diff --git a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotPerCellQC-1.png b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotPerCellQC-1.png
diff --git a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotScDblFinder-1.png b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotScDblFinder-1.png
diff --git a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plottDecontX-1.png b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plottDecontX-1.png
diff --git a/docs/articles/02_a_la_carte_workflow.html b/docs/articles/02_a_la_carte_workflow.html
diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/deHeatmap-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/deHeatmap-1.png
diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/markerHeatmap-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/markerHeatmap-1.png
diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/pathwayDEHeatmap-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/pathwayDEHeatmap-1.png
diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotCluster-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotCluster-1.png
diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotClusterAbundance-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotClusterAbundance-1.png
diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotTopHVG-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotTopHVG-1.png
diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/visVAM-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/visVAM-1.png
diff --git a/docs/articles/2d_embedding.html b/docs/articles/2d_embedding.html
diff --git a/docs/articles/batch_correction.html b/docs/articles/batch_correction.html
diff --git a/docs/articles/batch_correction_files/figure-html/batchVarAfter-1.png b/docs/articles/batch_correction_files/figure-html/batchVarAfter-1.png
diff --git a/docs/articles/batch_correction_files/figure-html/batchVarBefore-1.png b/docs/articles/batch_correction_files/figure-html/batchVarBefore-1.png
diff --git a/docs/articles/batch_correction_files/figure-html/umapAfter-1.png b/docs/articles/batch_correction_files/figure-html/umapAfter-1.png
diff --git a/docs/articles/batch_correction_files/figure-html/umapBefore-1.png b/docs/articles/batch_correction_files/figure-html/umapBefore-1.png
diff --git a/docs/articles/celda_curated_workflow.html b/docs/articles/celda_curated_workflow.html