| covered.k {TEQC} | R Documentation |
Calculates fraction of target bases covered by at least k reads
covered.k(coverageTarget, k = c(1, 2, 3, 5, 10, 20))
coverageTarget |
|
k |
integer vector of |
Named vector of same length as k giving the corresponding fractions of target bases
achieving coverages >= k
Manuela Hummel m.hummel@dkfz.de
coverage.target, coverage.hist, coverage.uniformity,
coverage.plot, 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)
covered.k(Coverage$coverageTarget, k=c(1,10,20))