visualizeSegments: Visualize segments

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Visualize segments

Description

The function takes a CNSegment object obtained from cnSegmentation and plot the bin signals and segments (as horizontal lines).

Usage

visualizeSegments(seg, to.plot = NULL, genes.to.label = NULL)

Arguments

seg	a CNSegment object
to.plot	chromosome to plot (by default plot all chromosomes)
genes.to.label	gene(s) to label

Details

require ggplot2, scales

Value

plot graphics

Examples

sesameDataCache()
## Not run: 
sdfs <- sesameDataGet('EPICv2.8.SigDF')
sdf <- sdfs[["K562_206909630040_R01C01"]]
seg <- cnSegmentation(sdf)
seg <- cnSegmentation(sdf, return.probe.signals=TRUE)
visualizeSegments(seg)
visualizeSegments(seg, to.plot=c("chr9","chr22"))
visualizeSegments(seg, genes.to.label=c("ABL1","BCR"))

## End(Not run)

sesameDataGet_resetEnv()

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.