Add reference sequence to a data.table

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