featureAlignedDistribution: plot distribution 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

plot distribution in the given feature ranges

Usage

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

Arguments

cvglists	Output of featureAlignedSignal or a list of SimpleRleList or RleList
feature.gr	An object of GRanges with identical width. If the width equal to 1, you can use upstream and downstream to set the range for plot. If the width not equal to 1, you can use zeroAt to set the zero point of the heatmap.
upstream, downstream	upstream or dwonstream from the feature.gr.
n.tile	The number of tiles to generate for each element of feature.gr, default is 100
zeroAt	zero point position of feature.gr
...	any paramters could be used by matplot

Value

invisible matrix of the plot.

Author(s)

Jianhong Ou

See Also

See Also as featureAlignedSignal, featureAlignedHeatmap

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))
  featureAlignedDistribution(cvglists, feature.gr, zeroAt=50, type="l")

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