plotMatrixSNP: Plot of methylation states dependencies

In methVisual: Methods for visualization and statistics on DNA methylation data

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

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.

Value

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

Author(s)

Arie Zackay <[e-mail]>, Christine Steinhoff <[e-mail]>

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"))

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: plotrix
Loading required package: gsubfn
Loading required package: proto
Loading required package: grid
Loading required package: sqldf
Loading required package: RSQLite
Warning message:
no DISPLAY variable so Tk is not available 
png 
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methVisual documentation built on April 28, 2020, 7:08 p.m.