featureAlignedSignal: extract signals in given ranges

Description Usage Arguments Value Author(s) See Also Examples

View source: R/featureAlignedSignal.R

Description

extract signals in the given feature ranges

Usage

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featureAlignedSignal(
  cvglists,
  feature.gr,
  upstream,
  downstream,
  n.tile = 100,
  ...
)

Arguments

cvglists

List of SimpleRleList or RleList

feature.gr

An object of GRanges with identical width.

upstream, downstream

Set the feature.gr to upstream and dwonstream from the center of the feature.gr if they are set.

n.tile

The number of tiles to generate for each element of feature.gr, default is 100

...

Not used.

Value

A list of matrix. In each matrix, each row record the signals for corresponding feature. rownames of the matrix show the seqnames and coordinates.

Author(s)

Jianhong Ou

See Also

See Also as featureAlignedHeatmap, featureAlignedDistribution

Examples

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  cvglists <- list(A=RleList(chr1=Rle(sample.int(5000, 100), 
                                      sample.int(300, 100))), 
                   B=RleList(chr1=Rle(sample.int(5000, 100), 
                                      sample.int(300, 100))))
  feature.gr <- GRanges("chr1", IRanges(seq(1, 4900, 100), width=100))
  featureAlignedSignal(cvglists, feature.gr)

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.