subsetByBidirectionality {CAGEfightR} | R Documentation |
A convenient wrapper around calcBidirectionality and subset.
subsetByBidirectionality(object, ...) ## S4 method for signature 'GRanges' subsetByBidirectionality( object, samples, inputAssay = "counts", outputColumn = "bidirectionality", minSamples = 0 ) ## S4 method for signature 'GPos' subsetByBidirectionality(object, ...) ## S4 method for signature 'RangedSummarizedExperiment' subsetByBidirectionality(object, ...)
object |
GRanges or RangedSummarizedExperiment: Unstranded clusters with peaks stored in the 'thick' column. |
... |
additional arguments passed to methods. |
samples |
RangedSummarizedExperiment: Sample-wise CTSSs stored as an assay. |
inputAssay |
character: Name of assay in samples holding input CTSS values. |
outputColumn |
character: Name of column in object to hold bidirectionality values. |
minSamples |
integer: Only regions with bidirectionality above this value are retained. |
object with bidirectionality values added as a column, and low bidirectionaly regions removed.
Other Subsetting functions:
subsetByComposition()
,
subsetBySupport()
Other Calculation functions:
calcBidirectionality()
,
calcComposition()
,
calcPooled()
,
calcShape()
,
calcSupport()
,
calcTPM()
,
calcTotalTags()
,
subsetByComposition()
,
subsetBySupport()
data(exampleCTSSs) data(exampleBidirectional) # Keep only clusters that are bidirectional in at least one sample: subsetByBidirectionality(exampleBidirectional, samples=exampleCTSSs)