methVisual (version 1.24.0)

plotMatrixSNP: Plot of methylation states dependencies

Description

Visulisation of dependencies between methylation states over explored bisulafite sequences

Usage

plotMatrixSNP(summeryMatrix,methData,file)

Arguments

summeryMatrix

see matrixSNP()

methData

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

file

String; quoted character string for specification of path and file name for saving the result. The result file is in .pdf format

Value

SNP Plot as pdf file saved in given path and name.

Details

The SNP Plot produce a visualisation of the cooccurrence between methylation states on CpGs over all explored sequences. The index of the CpGs is based on there position on genomic sequence.

Examples

## using methData

data(methData)
summeryMatrix <- matrixSNP(methData)

## using methData, file is the path to R home directory.
## In order to save plotMatrixSNP.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)
summary <- matrixSNP(methData)
plotMatrixSNP(summary,methData,
              file=file.path(BiqAnalyzer_path, "plotMatrixSNP.pdf"))