coverageFromBedGraph: read coverage from bedGraph files

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

Description

read coverage from bedGraph files and save as a list.

Usage

    coverageFromBedGraph(bedgraphs, tags, genome, 
                        hugeData=FALSE, BPPARAM=NULL, ...)

Arguments

bedgraphs	The file names of bedgraphs generated by bedtools. eg: bedtools genomecov -bg -split -ibam $bam -g mm10.size.txt > $bedgraph
tags	the names for each input bedgraphs
genome	an object of BSgenome
hugeData	is this dataset consume too much memory? if it is TRUE, the coverage will be saved into tempfiles.
BPPARAM	An optional 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.
...	parameters can be passed into tempfile. This is useful when you submit huge dataset to cluster.

Value

return a list of coverage for each bedgraph files. For each item in the list, it is a list of coverage for each chromosome. And the chromosome must start from "chr".

Author(s)

Jianhong Ou

Examples

    if(interactive()){
        library(BSgenome.Mmusculus.UCSC.mm10)
        path <- file.path(find.package("InPAS"), "extdata")
        bedgraphs <- file.path(path, "Baf3.extract.bedgraph")
        data(utr3.mm10)
        tags <- "Baf3"
        genome <- BSgenome.Mmusculus.UCSC.mm10
        coverage <- 
            coverageFromBedGraph(bedgraphs, tags, genome, hugeData=FALSE)
    }

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