normalize_scExp: Normalize counts

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

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))

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.