normalize_scExp: Normalize counts

Description Usage Arguments Value Examples

View source: R/preprocessing_filtering_reduction.R

Description

Normalize counts

Usage

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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

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

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