calcSupport {CAGEfightR} | R Documentation |
Calculate the number of samples expression a feature above a certain level. This number is refered to as the 'support'.
calcSupport( object, inputAssay = "counts", outputColumn = "support", unexpressed = 0 )
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. |
object with support added as a column in rowRanges.
Other Calculation functions:
calcBidirectionality()
,
calcComposition()
,
calcPooled()
,
calcShape()
,
calcTPM()
,
calcTotalTags()
,
subsetByBidirectionality()
,
subsetByComposition()
,
subsetBySupport()
data(exampleUnidirectional) # Count samples with at at least a single tags exampleUnidirectional <- calcSupport(exampleUnidirectional, inputAssay='counts', unexpressed=0) # Count number of samples with more than 1 TPM and save as a new column. exampleUnidirectional <- calcTPM(exampleUnidirectional, totalTags = 'totalTags') exampleUnidirectional <- calcSupport(exampleUnidirectional, inputAssay='TPM', unexpressed=1, outputColumn='TPMsupport')