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Map transcript IDs from a tx2gene table to a readcounts matrix

Source: R/map_functions.R
map_tx_to_readcounts.Rd

Assign transcript identifiers as row names of a transcript-level read counts matrix so downstream plotting functions can identify transcripts. The tx2gene mapping can be provided as a file path (TSV) or a data.frame with a `Transcript` column.

Usage

map_tx_to_readcounts(
  readcounts,
  tx2gene,
  tx_col = "Transcript",
  verbose = FALSE
)

Arguments

readcounts

A numeric matrix or data.frame of read counts (rows = transcripts).

tx2gene

Either a path to a tab-delimited file or a data.frame with at least a `Transcript` column.

tx_col

Name of the transcript ID column in `tx2gene` (default: 'Transcript').

verbose

Logical; print informative messages (default: FALSE).

Value

The input `readcounts` with rownames set to the transcript IDs.

Examples

readcounts <- matrix(1:4, nrow = 2, dimnames = list(NULL, c('s1', 's2')))
tx2gene <- data.frame(Transcript = c('tx1', 'tx2'), Gene = c('g1', 'g2'), stringsAsFactors = FALSE)
rc <- map_tx_to_readcounts(readcounts, tx2gene)
rownames(rc)
#> [1] "tx1" "tx2"