coverage.target {TEQC} | R Documentation |
Calculates average coverage over all target bases, average coverage for each target separately, and per-base coverage for all and for targeted bases
coverage.target(reads, targets, Offset = 0, perTarget = TRUE, perBase = TRUE)
reads |
|
targets |
|
Offset |
integer; add |
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 |
coverageAll |
|
coverageTarget |
|
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)