UTR3TotalCoverage: extract coverage of 3UTR for CP sites prediction

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Description

extract 3UTR coverage from totalCov according and GRanges object utr3.

Usage

UTR3TotalCoverage(utr3, totalCov, gcCompensation = NA, 
                  mappabilityCompensation = NA, 
                  FFT = FALSE, fft.sm.power = 20)

Arguments

utr3	an GRanges object. must be the output of utr3Annotation
totalCov	total coverage of each sample. must be the output of totalCoverage
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 frequence of FFT smooth.

Value

a list. level 1: chromosome; level 2: each transcripts; level3: data matrix

Author(s)

Jianhong Ou

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.