CompareWilcox {ChromSCape} | R Documentation |
CompareWilcox
CompareWilcox( dataMat = NULL, annot = NULL, ref_group = NULL, groups = NULL, featureTab = NULL, block = NULL, BPPARAM = BiocParallel::bpparam() )
dataMat |
A raw count matrix |
annot |
A cell annotation data.frame |
ref_group |
List with cells in reference group(s) |
groups |
List with cells in group(s) to test |
featureTab |
data.frame with feature annotation |
block |
Use a blocking factor to conteract batch effect ? |
BPPARAM |
BPPARAM object for multiprocessing. See bpparam for more informations. Will take the default BPPARAM set in your R session. |
A dataframe containing the foldchange and p.value of each feature
Eric Letouze & Celine Vallot & Pacome Prompsy
data("scExp") scExp_cf = correlation_and_hierarchical_clust_scExp(scExp) scExp_cf = choose_cluster_scExp(scExp_cf,nclust=2,consensus=FALSE) featureTab = as.data.frame(SummarizedExperiment::rowRanges(scExp_cf)) rownames(featureTab) = featureTab$ID ref_group = list("C1"=scExp_cf$cell_id[which(scExp_cf$cell_cluster=="C1")]) groups = list("C2"=scExp_cf$cell_id[which(scExp_cf$cell_cluster=="C2")]) myres = CompareWilcox(as.matrix(SingleCellExperiment::normcounts(scExp_cf)), annot=as.data.frame(SingleCellExperiment::colData(scExp_cf)), ref_group=ref_group,groups=groups, featureTab=featureTab)