readsPerTarget {TEQC} | R Documentation |
Counts the numbers of reads overlapping each target region
readsPerTarget(reads, targets, Offset = 0)
reads |
|
targets |
|
Offset |
integer; add |
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)