subsetBySupport {CAGEfightR} | R Documentation |
A convienient wrapper around calcSupport and subset.
subsetBySupport( object, inputAssay = "counts", outputColumn = "support", unexpressed = 0, minSamples = 1 )
object |
RangedSummarizedExperiment: CAGE data quantified at CTSS, cluster or gene-level. |
inputAssay |
character: Name of assay holding input expression values. |
outputColumn |
character: Name of column in rowRanges to hold support values. |
unexpressed |
numeric: Support will be calculated based on features larger than this cutoff. |
minSamples |
numeric: Only features with support in more than this number of samples will be kept. |
RangedSummarizedExperiment with support added as a column in rowRanges and features with less support than minSamples removed.
Other Subsetting functions:
subsetByBidirectionality()
,
subsetByComposition()
Other Calculation functions:
calcBidirectionality()
,
calcComposition()
,
calcPooled()
,
calcShape()
,
calcSupport()
,
calcTPM()
,
calcTotalTags()
,
subsetByBidirectionality()
,
subsetByComposition()
data(exampleBidirectional) # Keep clusters with at least one tag in two samples subsetBySupport(exampleBidirectional) # Keep clusters with at least two tags in four samples subsetBySupport(exampleBidirectional, unexpressed=1, minSamples=2)