normalize_scExp {ChromSCape}R Documentation

Normalize counts

Description

Normalize counts

Usage

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

Arguments

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.

Value

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

Examples

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


[Package ChromSCape version 1.0.0 Index]