| 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')