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))