Target capture sensitivity

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Description

Calculates fraction of target bases covered by at least k reads

Usage

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covered.k(coverageTarget, k = c(1, 2, 3, 5, 10, 20))

Arguments

coverageTarget

RleList containing Rle vectors of per-target-base coverages for each chromosome, i.e. coverageTarget output from coverage.target

k

integer vector of k-values for which to show fraction of target bases with coverage >= k

Value

Named vector of same length as k giving the corresponding fractions of target bases achieving coverages >= k

Author(s)

Manuela Hummel m.hummel@dkfz.de

See Also

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

Examples

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## 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))