calcShape: Calculate Tag Cluster shapes

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Description

Apply a shape-function to the pooled CTSS signal of every Tag Cluster (TC).

Usage

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, ...)

Arguments

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).

Value

object with calculated shape statistics added as a column in rowData (or mcols).

See Also

Other Calculation functions: calcBidirectionality(), calcComposition(), calcPooled(), calcSupport(), calcTPM(), calcTotalTags(), subsetByBidirectionality(), subsetByComposition(), subsetBySupport()

Other Shape functions: shapeEntropy(), shapeIQR(), shapeMean()

Examples

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!

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.