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

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

[Package ChromSCape version 1.2.62 Index]