get_UTR3TotalCov: extract coverage of 3' UTR for CP sites prediction

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

extract coverage of 3' UTR for CP sites prediction

Description

extract 3' UTR coverage from totalCov according to the GenomicRanges::GRanges object utr3.

Usage

get_UTR3TotalCov(
  chr.utr3,
  chr.totalCov,
  gcCompensation = NA,
  mappabilityCompensation = NA,
  FFT = FALSE,
  fft.sm.power = 20
)

Arguments

chr.utr3	An object of GenomicRanges::GRanges. It must be an element of the output of extract_UTR3Anno() for a given chromosome.
chr.totalCov	total coverage for each condition of a given chromosome. It must be an output of get_totalCov()
mappabilityCompensation	mappability compensation vector. Not support yet.
FFT	Use FFT smooth or not.
fft.sm.power	the cut-off frequency of FFT smooth.
gcCompensationensation	GC compensation vector. Not support yet.

Value

path to a file storing the UTR3 total coverage for a given chromosome/scaffold

Author(s)

Jianhong Ou

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.