read coverage from bedGraph files

Description

read coverage from bedGraph files and save as a list.

Usage

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

Arguments

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)
    }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(InPAS)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/InPAS/coverageFromBedGraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coverageFromBedGraph
> ### Title: read coverage from bedGraph files
> ### Aliases: coverageFromBedGraph
> ### Keywords: misc
> 
> ### ** Examples
> 
> #    if(interactive()){
>         library(BSgenome.Mmusculus.UCSC.mm10)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
>         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)
> #    }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>