readsPerTarget: Numbers of reads per target
In hummelma/TEQC: Quality control for target capture experiments

Description Usage Arguments Value Note Author(s) See Also Examples

Counts the numbers of reads overlapping each target region

1	readsPerTarget(reads, targets, Offset = 0)

`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

The input RangedData table targets with an additional 'values' column containing numbers of reads overlapping each target

As reads input also the mappingReads output of function fraction.reads.target can be used to speed up calculation. In this case, make sure that targets and Offset parameters were the same in fraction.reads.target as then specified in readsPerTarget.

Manuela Hummel m.hummel@dkfz.de

coverage.target, fraction.reads.target, 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)

## number of reads per target
readsPerTarget(reads, targets)