make.wigfiles {TEQC} | R Documentation |
Prepares wiggle files with (non-zero) per-base coverages for the upload and visualization with genome browsers
make.wigfiles(coverageAll, chroms, trackname = "Coverage", filename = "Coverage")
coverageAll |
|
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"))