get_UTR3TotalCov {InPAS}R Documentation

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

Arguments

utr3

An object of GenomicRanges::GRangesList. It must be the output of extract_UTR3Anno()

totalCov

total coverage for each sample. It must be a list of the output of get_totalCov()

BPPARAM

an optional BiocParallel::BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to bplapply. It can be set to NULL or bpparam()

gcCompensation

GC compensation vector. Not support yet.

mappabilityCompensation

mappability compensation vector. Not support yet.

FFT

Use FFT smooth or not.

fft.sm.power

the cut-off frequency of FFT smooth.

Value

A list containing total coverage for each 3' UTR.

seqname

chromosome/scaffold name

transcript1

data matrix containing summarized View for transcript1

transcript2

data matrix containing summarized View for transcript2

transcriptN

data matrix containing summarized View for transcriptN

Author(s)

Jianhong Ou


[Package InPAS version 2.2.0 Index]