normalize_scExp {ChromSCape}R Documentation

Normalize counts

Description

Normalize counts

Usage

normalize_scExp(
  scExp,
  type = c("CPM", "TFIDF", "RPKM", "TPM", "feature_size_only")
)

Arguments

scExp

A SingleCellExperiment object.

type

Which normalization to apply. Either 'CPM', 'TFIDF','RPKM', 'TPM' or 'feature_size_only'. Note that for all normalization by size (RPKM, TPM, feature_size_only), the features must have defined genomic coordinates.

Value

A SingleCellExperiment object containing normalized counts. (See ?normcounts())

Examples

raw <- create_scDataset_raw()
scExp = create_scExp(raw$mat, raw$annot)
scExp = normalize_scExp(scExp)
head(SingleCellExperiment::normcounts(scExp))


[Package ChromSCape version 1.4.0 Index]