trimToPercentiles: Trim width of TCs to expression percentiles

Description Usage Arguments Value See Also Examples

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

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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

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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 March 14, 2019, 10:56 p.m.