Description Usage Arguments Value Author(s) Examples
View source: R/support_functions.R
CompareWilcox
1 2 3 4 5 6 7 8 |
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 ? |
A dataframe containing the foldchange and p.value of each feature
Eric Letouze & Celine Vallot
1 2 3 4 5 6 7 8 9 10 | 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)
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