| 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,GRanges' calcShape(object, pooled, outputColumn = "IQR", shapeFunction = shapeIQR, ...) ## S4 method for signature 'RangedSummarizedExperiment,GRanges' calcShape(object, pooled, ...) ## S4 method for signature 'GRanges,RangedSummarizedExperiment' calcShape(object, pooled, ...) ## S4 method for signature 'GRanges,GPos' 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(),
shapeMean()
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!