featureAlignedSignal: extract signals in given ranges

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

extract signals in the given feature ranges

Usage

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

  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.