trimToPeak {CAGEfightR}R Documentation

Trim width of TCs by distance from TC peak

Description

Trim the width of TCs by distance from the TC peaks.

Usage

trimToPeak(object, pooled, ...)

## S4 method for signature 'GRanges,GenomicRanges'
trimToPeak(object, pooled, upstream,
  downstream, peaks = "thick")

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

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


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

Arguments

object

GenomicRanges or RangedSummarizedExperiment: Tag clusters.

pooled

GenomicRanges or RangedSummarizedExperiment: Basepair-wise pooled CTSS (stored in the score column).

...

additional arguments passed to methods.

upstream

integer: Maximum upstream distance from TC peak.

downstream

integer: Maximum downstream distance from TC peak.

peaks

character: Name of column in TCs holding TC peaks as an IRanges.

Value

data.frame with two columns: threshold and nTCs (number of Tag Clusters)

See Also

Other Clustering functions: clusterBidirectionally, clusterUnidirectionally, trimToPercentiles, tuneTagClustering

Other Trimming functions: trimToPercentiles

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)

# Trim to +/- 10 bp of TC peak
trimToPeak(TCs, pooled=exampleCTSSs, upstream=10, downstream=10)

[Package CAGEfightR version 1.0.0 Index]