calcBidirectionality {CAGEfightR} | R Documentation |
For each cluster, calculate how many individual samples shows transcription in both directions. This is refered to as the 'bidirectionality'. Clusters must be unstranded (*) and have a midpoint stored in the thick column
calcBidirectionality(object, ...) ## S4 method for signature 'GRanges' calcBidirectionality( object, samples, inputAssay = "counts", outputColumn = "bidirectionality" ) ## S4 method for signature 'GPos' calcBidirectionality(object, ...) ## S4 method for signature 'RangedSummarizedExperiment' calcBidirectionality(object, ...)
object |
GenomicRanges or RangedSummarizedExperiment: Unstranded clusters with midpoints 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. |
object returned with bidirectionality scores added in rowData (or mcols).
Other Calculation functions:
calcComposition()
,
calcPooled()
,
calcShape()
,
calcSupport()
,
calcTPM()
,
calcTotalTags()
,
subsetByBidirectionality()
,
subsetByComposition()
,
subsetBySupport()
data(exampleCTSSs) data(exampleBidirectional) calcBidirectionality(exampleBidirectional, samples=exampleCTSSs)