Complete a DT object missing genes

A function that adds the genomic and transcriptomic coordinates of genes with no data in a data.table generated by the tx_coverageDT, tx_nucFreqDT, and tx_covNucFreqDT functions.

Usage

tx_complete_DT(DT, geneAnnot, genome = NULL, nCores = 1)

Arguments

DT

data.table. A table as output by the tx_makeDT_coverage(), tx_makeDT_nucFreq() or tx_makeDT_covNucFreq() functions.

geneAnnot

GRanges. Gene annotation as loaded by tx_load_bed().

genome

list. The full reference genome sequences, as loaded by tx_load_genome() or prepackaged by BSgenome, see ?BSgenome::available.genomes

nCores

integer. Number of cores to run the function with. Multicore capability not available in Windows OS.

Value

data.table

Details

This function is meant to equalize datasets which don't contain some genes, as such the order of the genes is the same as in the GRanges object used as gene annotation.