calcPooled {CAGEfightR} | R Documentation |
Sum expression of features across all samples to obtain a 'pooled' signal.
calcPooled(object, inputAssay = "TPM", outputColumn = "score")
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 pooled expression. |
object with pooled expression added as a column in rowRanges.
Other Calculation functions:
calcBidirectionality()
,
calcComposition()
,
calcShape()
,
calcSupport()
,
calcTPM()
,
calcTotalTags()
,
subsetByBidirectionality()
,
subsetByComposition()
,
subsetBySupport()
data(exampleCTSSs) # Calculate TPM using supplied total number of tags: exampleCTSSs <- calcTPM(exampleCTSSs, totalTags='totalTags') # Sum TPM values over samples: calcPooled(exampleCTSSs)