Skip to contents

Get metagene regions

tx_get_metageneRegions.Rd

Summarizes the values of a column(s) into a selected number of bins per gene structure region (5'UTR, CDS, 3'UTR).

Usage

tx_get_metageneRegions(
  txDT,
  geneAnnot,
  colVars,
  nBins_5UTR,
  nBins_CDS = NULL,
  nBins_3UTR = NULL,
  nCores = 1
)

Arguments

txDT

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().

colVars

character. Names of columns for which values will be extracted

nBins_5UTR

integer. Number of bins into which allocate data on 5'UTR regions

nBins_CDS

integer. Number of bins into which allocate data on CDS regions

nBins_3UTR

integer. Number of bins into which allocate data on 3'UTR regions

nCores

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

Value

list of matrices for each colVar