calcShape {CAGEfightR} | R Documentation |
Apply a shape-function to the pooled CTSS signal of every Tag Cluster (TC).
calcShape(object, pooled, ...) ## S4 method for signature 'GRanges,GenomicRanges' calcShape(object, pooled, outputColumn = "IQR", shapeFunction = shapeIQR, ...) ## S4 method for signature 'RangedSummarizedExperiment,GenomicRanges' calcShape(object, pooled, ...) ## S4 method for signature 'GRanges,RangedSummarizedExperiment' calcShape(object, pooled, ...) ## S4 method for signature ## 'RangedSummarizedExperiment,RangedSummarizedExperiment' calcShape(object, pooled, ...)
object |
GenomicRanges or RangedSummarizedExperiment: TCs. |
pooled |
GenomicRanges or RangedSummarizedExperiment: Pooled CTSS as the score column. |
... |
additional arguments passed to shapeFunction. |
outputColumn |
character: Name of column to hold shape statistics. |
shapeFunction |
function: Function to apply to each TC (See details). |
object with calculated shape statistics added as a column in rowData (or mcols).
Other Calculation functions: calcBidirectionality
,
calcComposition
, calcPooled
,
calcSupport
, calcTPM
,
calcTotalTags
,
subsetByBidirectionality
,
subsetByComposition
,
subsetBySupport
Other Shape functions: shapeEntropy
,
shapeIQR
, shapeMultimodality
data(exampleCTSSs) data(exampleUnidirectional) # Calculate pooled CTSSs using pre-calculated number of total tags: exampleCTSSs <- calcTPM(exampleCTSSs, totalTags='totalTags') exampleCTSSs <- calcPooled(exampleCTSSs) # Calculate shape statistics calcShape(exampleUnidirectional, pooled=exampleCTSSs, outputColumn='entropy', shapeFunction=shapeEntropy) calcShape(exampleUnidirectional, pooled=exampleCTSSs, outputColumn='IQR', shapeFunction=shapeIQR, lower=0.2, upper=0.8) # See the vignette for how to implement custom shape functions!