Cooccurrence: Visualization of binary methylation data

In methVisual: Methods for visualization and statistics on DNA 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

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.

Value

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

Author(s)

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

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")) 

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 
      LABEL_Y_AXIS       Experiment
1                1   QC_seq_B.fasta
2                2   QC_seq_C.fasta
3                3   QC_seq_E.fasta
4                4   QC_seq_G.fasta
5                5   QC_seq_H.fasta
6                6   QC_seq_I.fasta
7 coocureceLolipop coocureceLolipop

methVisual documentation built on April 28, 2020, 7:08 p.m.