plotAvgViewpoint: Plot coverage around a set of virtual 4C viewpoints

Description Usage Arguments Value Examples

View source: R/viewPoints.R

Description

Plots summarised coverage of interactions around a set of viewpoints, e.g. promoters. This function requires the output of 'viewPoint()' as input.

Usage

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plotAvgViewpoint(x, left_dist = 1e+05, right_dist = 1e+05,
  ylab = "Average signal", xlab = "Relative position", fix = "center",
  ...)

Arguments

x

A GInteractions object which is output from viewPoint

left_dist

Distance 'left' of interactions to consider, in bp.

right_dist

Distance 'right' of interactions to consider, in bp.

ylab

Y axis label.

xlab

X axis label.

fix

One of "center", "start", "end". Passed to 'resize'. Interaction distances are calculated relative to this part of the bait.

...

additional arguments to plot

Value

Coverage that is plotted (invisibly)

Examples

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data(hic_example_data)
library(GenomicRanges)
pos <- GRanges(seqnames="chr15", ranges=IRanges(start=59477709, end=59482708))
region <- GRanges(seqnames="chr15", ranges=IRanges(start=58980209, end=59980208))
vp <- viewPoint(hic_example_data, pos, region)
plotAvgViewpoint(vp, left_dist = 1000000, right_dist = 100000)

Bioconductor-mirror/GenomicInteractions documentation built on June 23, 2017, 6:23 p.m.