MethLollipops: "Lollipops" Methylation plot

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

Description

Visualization of methylation patterns in terms of "Lollipops" plot

Usage

MethLollipops(methData)

Arguments

methData

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

Details

The lollipops plot allows the user to study the genomic localization and states of CpG sites. Each circle marks a CpG site under study. Full circles display methylated CpGs and the non filled ones stand for non methylated CpG states. The examined sequences are aligned with respect to the genomic sequence in order to allow for an intuitive visualization of methylation states according to their genomic position.

Value

Returns a "lollipop" plot

Author(s)

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

Examples

data("methData")
MethLollipops(methData)

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
Could not load tcltk.  Will use slower R code instead.
Loading required package: grid
Loading required package: sqldf
Loading required package: RSQLite
  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       refSeq refernceSequence

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