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]