methVisual (version 1.24.0)

Cooccurrence: Visualization of binary methylation data

Description

Visualization of binary methylation data including neighboured cooccurrence

Usage

Cooccurrence(methData,file,real,lolli)

Arguments

methData

List; contains information on the pairwise alignments, and methylated CpG motifs.

file

String; path and file name for saving the result. Default format is .pdf

real

logical; real position (real=TRUE) or relative position (real=FLASE) according to the reference sequence

lolli

Integer; size of lollipops

Value

summary plot that will be saved by default as pdf file under the given path and name

Details

Visualization of methylation states using lollipop graphs, percentage of methylation across experiments and value of neighboured cooccurrence due to calculation of spearman correlation. Every single CpG site is marked with a circle with the following characteristic, a filled circle represents a methylated CpG and an empty circle a non methylated one. The modification in methVisual lollipop plot is the calculation and visualization of dependencies (also known as cooccurrence) between neighbored methylated CpG site and non methylated CpG site. That means, given a set of bisulfite sequenced clones one would like to detect subgroups where specific CpG sites always occur coordinately either methylated or non methylated.

Examples

## using methData, file is the path to R home directory.
## In order to save Cooccurrence.pdf, make sure that you have writing 
## permission under R.home() directory. If you do not have permission
## choose your own path. 
#dir.create(file.path(R.home(component="home"),"/BiqAnalyzer")) 
BiqAnalyzer_path <- file.path(tempdir(), "BiqAnalyzer")
dir.create(BiqAnalyzer_path)
data(methData)
Cooccurrence(methData,file=file.path(BiqAnalyzer_path, "Cooccurrence.pdf"))