tx_add_refSeqDT: Add reference sequence to a data.table

In AngelCampos/txtools: An R package facilitating analysis of RNA modifications, structures, and interactions

Add reference sequence to a data.table

Description

Adds a column of characters representing the corresponsing nucleotide at the reference genome position, considering the strand of the transcript. The input DT must be the output, or resemble it, of the

Usage

tx_add_refSeqDT(DT, genome, geneAnnot, nCores = 1)

Arguments

DT	data.table. A table as output by the tx_makeDT_coverage(), tx_makeDT_nucFreq() or tx_makeDT_covNucFreq() functions.
genome	list. The full reference genome sequences, as loaded by tx_load_genome() or prepackaged by BSgenome, see ?BSgenome::available.genomes
geneAnnot	GRanges. Gene annotation as loaded by tx_load_bed().
nCores	integer. Number of cores to run the function with. Multicore capability not available in Windows OS.

Value

data.table

AngelCampos/txtools documentation built on Sept. 16, 2024, 10:25 p.m.