coverage.target: Calculates read coverage
In hummelma/TEQC: Quality control for target capture experiments

Description Usage Arguments Value Author(s) See Also Examples

Calculates average coverage over all target bases, average coverage for each target separately, and per-base coverage for all and for targeted bases

1	coverage.target(reads, targets, Offset = 0, perTarget = TRUE, perBase = TRUE)

`reads`	`RangedData` table containing positions of sequenced reads, i.e. output from `get.reads`
`targets`	`RangedData` table containing positions of target regions, i.e. output from `get.targets`
`Offset`	integer; add `Offset` bases on both sides to targeted regions and potentially collapse resulting overlapping target regions
`perTarget`	if TRUE, coverage average and standard deviation per target are calculated and returned
`perBase`	if TRUE, the per-base coverages i) only for targeted bases and ii) for all sequenced and/or targeted bases, are returned

A list is returned with elements

`avgTargetCoverage`	average coverage over all target bases
`targetCoverageSD`	standard deviation of coverage of all target bases
`targetCoverageQuantiles`	0% (minium), 25%, 50% (median), 75% and 100% (maximum) quantiles of coverage of all target bases
`targetCoverages`	Input `RangedData` table `targets` with two additional 'values' columns `avgCoverage` and `coverageSD`. The former contains the average coverage for each target, the latter the respective coverage standard deviation. Only returned if `perTarget` equals `TRUE`.
`coverageAll`	`RleList` containing a `Rle` vector for each chromosome with coverages for all bases that are sequenced and/or within a targeted; only returned if `perBase` equals `TRUE`
`coverageTarget`	`RleList` containing a `Rle` vector for each chromosome with coverages for target bases only; only returned if `perBase` equals `TRUE`

Manuela Hummel m.hummel@dkfz.de

covered.k, 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)

## total average, per-base and per-target coverages
Coverage <- coverage.target(reads, targets)