Get Salmon Counts — salmon_counts • RNAsum

Get salmon counts via tximport.

Usage

salmon_counts(x, tx2gene = NULL)

Arguments

x: Path to quant.sf or quant.genes.sf file with abundances. See tximport::tximport.
tx2gene: data.frame with tx_name and gene_id columns. See tximport::tximport.

Value

Tibble with the counts per gene transcript, or NULL if any of the input params are NULL.

Examples

x <- system.file("rawdata/test_data/dragen/TEST.quant.sf", package = "RNAsum")
tx2gene <- NULL
(sc <- salmon_counts(x, tx2gene)) # NULL since no tx2gene specified
#> NULL