NormalizeTPM {ADImpute} | R Documentation

## TPM normalization

### Description

`NormalizeTPM` performs TPM normalization, with possibility to log the result

### Usage

    NormalizeTPM(data, sce = NULL, tr_length = NULL, log = FALSE,
    scale = 1, pseudo.count = 1)

### Arguments

`data` | matrix; raw data (genes as rows and samples as columns)
`sce` | SingleCellExperiment; raw data
`tr_length` | data.frame with at least 2 columns: 'hgnc_symbol' and 'transcript_length'
`log` | logical; log TPMs?
`scale` | integer; scale factor to divide TPMs by
`pseudo.count` | numeric; if `log = T`, value to add to TPMs in order to avoid taking `log(0)`

### Details

Gene length is estimated as the median of the lengths of all transcripts for each gene, as obtained from biomaRt. Genes for which length information cannot be found in biomaRt are dropped.

### Value

matrix; normalized data (for transcript length and library size)

### Examples

    demo <- NormalizeTPM(ADImpute::demo_data)

[Package ADImpute version 1.2.0 Index]