NormalizeTPM: TPM normalization

In beyergroup/ADImpute: Adaptive Dropout Imputer (ADImpute)

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)

beyergroup/ADImpute documentation built on Dec. 19, 2021, 8:48 a.m.