CompareWilcox

Source: R/support_functions.R

CompareWilcox

CompareWilcox(
  dataMat = NULL,
  annot = NULL,
  ref_group = NULL,
  groups = NULL,
  featureTab = NULL,
  block = NULL,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

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.

Value

A dataframe containing the foldchange and p.value of each feature

Author

Eric Letouze & Celine Vallot & Pacome Prompsy

Examples

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)