Calculates read coverage

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Description

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

Usage

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

Arguments

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

Value

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

Author(s)

Manuela Hummel m.hummel@dkfz.de

See Also

covered.k, 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)

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