normalize_scExp: Normalize counts

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

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))

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.