NormalizeTPM {ADImpute} | R Documentation |
NormalizeTPM
performs TPM normalization, with possibility
to log the result
NormalizeTPM(data, sce = NULL, tr_length = NULL, log = FALSE, scale = 1, pseudo.count = 1)
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 |
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.
matrix; normalized data (for transcript length and library size)
demo <- NormalizeTPM(ADImpute::demo_data)