covThreshold: calculate the cutoff threshold of coverage

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

Description

calculate the cutoff threshold of coverage for long form and short form

Usage

covThreshold(coverage, genome, txdb, utr3, 
                         chr="chr1", hugeData, groupList)

Arguments

coverage	coverage for each sample, output of coverageFromBedGraph
genome	an object of BSgenome
txdb	an object of TxDb
utr3	output of utr3Annotation
chr	chromosome to be used for calculation, default is "chr1"
hugeData	is this dataset consume too much memory? if it is TRUE, the coverage will be saved into tempfiles.
groupList	group list of tag names

Value

a numeric vector

Author(s)

Jianhong Ou

See Also

CPsite_estimation

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