CompareWilcox {ChromSCape} | R Documentation

## CompareWilcox

### Description

CompareWilcox

### Usage

    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(s)

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)

[Package ChromSCape version 1.2.62 Index]