make.wigfiles: Creates wiggle files with per-base coverages
In hummelma/TEQC: Quality control for target capture experiments

Description Usage Arguments Details Value Author(s) See Also Examples

Prepares wiggle files with (non-zero) per-base coverages for the upload and visualization with genome browsers

1	make.wigfiles(coverageAll, chroms, trackname = "Coverage", filename = "Coverage")

`coverageAll`	`RleList` containing `Rle` vectors of per-base coverages for each chromosome, i.e. `coverageAll` output of `coverage.target`
`chroms`	vector of chromosome names for which to produce wiggle files; if missing wiggle files will be produced for all chromosomes on which there are reads
`trackname`	trackname for wiggle file header
`filename`	part of output wiggle file name. Respective chromosome number and '.wig' will be added

Only non-zero coverages will be listed

One or more wiggle files listing per-base (non-zero) read coverages

Manuela Hummel m.hummel@dkfz.de

coverage.target, coverage.plot, covered.k, coverage.hist, coverage.uniformity, coverage.targetlength.plot

## get reads and targets
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

## calculate per-base coverages
Coverage <- coverage.target(reads, targets, perBase=TRUE)

## create wiggle files for read coverages on chromsomes 13 and 17
make.wigfiles(Coverage$coverageAll, chroms=c("chr13", "chr17"))