fraction.reads.target: Target capture specificity
In hummelma/TEQC: Quality control for target capture experiments

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

Calculates the fraction of reads that align to target regions. Can also be used to retrieve those reads mapping to targets.

1	fraction.reads.target(reads, targets, Offset = 0, mappingReads = FALSE)

`reads`	`RangedData` table containing positions of sequenced reads, i.e. output of `get.reads`. Alternatively, for paired-end data, it can be the output of `reads2pairs` when fraction of on-target read pairs shall be calculated instead of fraction of single on-target 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
`mappingReads`	if `TRUE`, reduced `RangedData` table with only those reads mapping to target regions is returned. When `reads` is output of `reads2pairs`, `mappingReads` will be the corresponding subset of on-target read pairs.

If mappingReads equals FALSE, just the fraction of reads / read pairs mapping to targets is returned. When reads contains all single reads (i.e. is output of get.reads), this is the number of target-overlapping reads, divided by the number of all single reads. When reads contains read pairs (i.e. is output of reads2pairs), it is the number of read pairs with at least one target-overlapping read, divided by the number of read pairs (= half the number of reads). In case of small targets and large insert sizes the two reads of a pair could be located on both sides of the target without overlap, respectively. Still, the read pair will be counted as on-target, since the corresponding DNA molecule was covering the target.

If mappingReads equals TRUE, a list is returned with elements

`onTargetFraction`	fraction of reads / read pairs mapping to targets
`mappingReads`	`RangedData` table containing positions of the reads / read pairs mapping to target regions

With the output from fraction.target and fraction.reads.target the 'enrichment' of the target capture experiment can be calculated as 'fraction of on-target reads / fraction of target within genome'

Manuela Hummel m.hummel@dkfz.de

fraction.target, get.reads, reads2pairs, get.targets

## 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)

## fraction of on-target reads
fraction.reads.target(reads, targets)