plotAbsMethyl: Plot number mathylation on CpGs positions

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

Description

Plot of absolute/relative number of mathylation on aligned CpGs positions

Usage

plotAbsMethyl(methData,real)

Arguments

methData	List; contains information on the pairwise alignments, and methylated CpG motifs.
real	real position (real=TRUE) or relative position (real=FLASE) on reference sequence

Details

This function generates a plot of the absolute number of methylation in all CpG sites over all examined sequences. It returns a vector with the absolute number of methylation sites of all examined clone sequences. The user supplies a list object containing information about the pairwise alignments, and methylated CpG sites as calculated by MethAlignNW() or makeDataMethGFF(). The user can display the absolute number of methylation over the CpG sites according to their relative position on the reference sequence.

Value

A vector with the absolute/relative number of methylation on genomic sequence CpG positions over all examined sequences

Author(s)

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

Examples

## using methData
data(methData)
plotAbsMethyl(methData,real=FALSE)

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