trimToPercentiles: Trim width of TCs to expression percentiles

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

Description

Given a set of TCs and genome-wide CTSS coverage, reduce the width of TC until a certain amount of expression has been removed.

Usage

trimToPercentiles(object, pooled, ...)

## S4 method for signature 'GRanges,GRanges'
trimToPercentiles(object, pooled, percentile = 0.1, symmetric = FALSE)

## S4 method for signature 'GRanges,GPos'
trimToPercentiles(object, pooled, ...)

## S4 method for signature 'RangedSummarizedExperiment,GenomicRanges'
trimToPercentiles(object, pooled, ...)

## S4 method for signature 'GRanges,RangedSummarizedExperiment'
trimToPercentiles(object, pooled, ...)

## S4 method for signature 
## 'RangedSummarizedExperiment,RangedSummarizedExperiment'
trimToPercentiles(object, pooled, ...)

Arguments

object	GenomicRanges or RangedSummarizedExperiment: TCs to be trimmed.
pooled	GenomicRanges or RangedSummarizedExperiment: CTSS coverage.
...	additional arguments passed to methods.
percentile	numeric: Fraction of expression to remove from TCs.
symmetric	logical: Whether to trim the same amount from both edges of the TC (TRUE) or always trim from the least expressed end (FALSE).

Value

GRanges with trimmed TCs, including recalculated peaks and scores.

See Also

Other Clustering functions: clusterBidirectionally(), clusterUnidirectionally(), trimToPeak(), tuneTagClustering()

Other Trimming functions: trimToPeak()

Examples

data(exampleCTSSs)
data(exampleBidirectional)

# Calculate pooled CTSSs
exampleCTSSs <- calcTPM(exampleCTSSs, totalTags='totalTags')
exampleCTSSs <- calcPooled(exampleCTSSs)

# Choose a few wide clusters:
TCs <- subset(exampleUnidirectional, width >= 100)

# Symmetric trimming (same percentage from each side):
TCs_sym <- trimToPercentiles(TCs, pooled=exampleCTSSs, symmetric=FALSE)

# Assymmetric trimming (always trim from lowest side):
TCs_asym <- trimToPercentiles(TCs, pooled=exampleCTSSs, symmetric=TRUE)

# Compare the two results sets of widths:
summary(width(TCs_sym) - width(TCs_asym))

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