normalize_scExp {ChromSCape} | R Documentation |
Normalize counts
normalize_scExp(scExp, type = c("RPKM", "CPM", "TPM", "feature_size_only"))
scExp |
A SingleCellExperiment object. |
type |
Which normalization to apply. Either 'RPKM', 'CPM', 'TPM' or 'feature_size_only'. Note that for all normalization by size (RPKM, TPM, feature_size_only), the features must have defined genomic coordinates. |
A SingleCellExperiment object containing normalized counts. (See ?normcounts())
scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot) scExp = normalize_scExp(scExp) head(SingleCellExperiment::normcounts(scExp))