calcTPM {CAGEfightR} | R Documentation |
Normalize CAGE-tag counts into TPM values.
calcTPM( object, inputAssay = "counts", outputAssay = "TPM", totalTags = NULL, outputColumn = "totalTags" )
object |
RangedSummarizedExperiment: CAGE data quantified at CTSS, cluster or gene-level. |
inputAssay |
character: Name of assay holding input expression values. |
outputAssay |
character: Name of assay to hold TPM values. |
totalTags |
character or NULL: Column in colData holding the total number of tags for each samples. If NULL, this will be calculated using calcTotalTags. |
outputColumn |
character: Name of column in colData to hold number of total tags, only used if totalTags is NULL. |
object with TPM-values added as a new assay. If totalTags is NULL, total tags added as a column in colData.
Other Calculation functions:
calcBidirectionality()
,
calcComposition()
,
calcPooled()
,
calcShape()
,
calcSupport()
,
calcTotalTags()
,
subsetByBidirectionality()
,
subsetByComposition()
,
subsetBySupport()
data(exampleUnidirectional) # Calculate TPM: calcTPM(exampleUnidirectional) # Use pre-calculated total number of tags: calcTPM(exampleUnidirectional, outputAssay='TPMsupplied', totalTags='totalTags')