tx_get_metageneRegions: Get metagene regions

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

Get metagene regions

Description

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

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