Read counting for several range sets

Description

Convenience function to perform read counting iteratively for serveral range sets, e.g. peak range sets or feature types. Internally, the read counting is performed with the summarizeOverlaps function from the GenomicAlignments package. The resulting count tables are directly saved to files.

Usage

countRangeset(bfl, args, format="tabular", ...)

Arguments

Value

Named character vector containing the paths from outpaths(args) to the resulting count table files.

Author(s)

Thomas Girke

See Also

summarizeOverlaps

Examples

## Paths to BAM files
param <- system.file("extdata", "bowtieSE.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args_bam <- systemArgs(sysma=param, mytargets=targets)
bfl <- BamFileList(outpaths(args_bam), yieldSize=50000, index=character())

## Not run: 
## SYSargs with paths to range data and count files
args <- systemArgs(sysma="param/count_rangesets.param", mytargets="targets_macs.txt")

## Iterative read counting
countDFnames <- countRangeset(bfl, args, mode="Union", ignore.strand=TRUE)
writeTargetsout(x=args, file="targets_countDF.txt", overwrite=TRUE)


## End(Not run)

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.
You are welcome to redistribute it under certain conditions.
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(systemPipeR)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/systemPipeR/countRangeset.Rd_%03d_medium.png", width=480, height=480)
> ### Name: countRangeset
> ### Title: Read counting for several range sets
> ### Aliases: countRangeset
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Paths to BAM files
> param <- system.file("extdata", "bowtieSE.param", package="systemPipeR")
> targets <- system.file("extdata", "targets.txt", package="systemPipeR")
> args_bam <- systemArgs(sysma=param, mytargets=targets)
There were 18 warnings (use warnings() to see them)
> bfl <- BamFileList(outpaths(args_bam), yieldSize=50000, index=character())
> 
> ## Not run: 
> ##D ## SYSargs with paths to range data and count files
> ##D args <- systemArgs(sysma="param/count_rangesets.param", mytargets="targets_macs.txt")
> ##D 
> ##D ## Iterative read counting
> ##D countDFnames <- countRangeset(bfl, args, mode="Union", ignore.strand=TRUE)
> ##D writeTargetsout(x=args, file="targets_countDF.txt", overwrite=TRUE)
> ##D 
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>