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Last data update: 2014.03.03

R: Generate Heatmap of the given methylation data.

methHeatmap

R Documentation

Generate Heatmap of the given methylation data.

Description

Heatmaps are the way of visualizing methylation statuses of a sample. This function allows user to visualize methylation statuses at each CpG site for every sequence available in pool.

Usage

methHeatmap(Sample, yl = "", plot = TRUE, title = "")

Arguments

`Sample`	Matrix from methAlign. Also matrix where columns represents Cytosine of CpG sites and rows represents sequences.
`yl`	Ylabel for heatmap
`plot`	Boolean. If plot == FALSE, function will return a matrix of 1s and 0s. If plot == TRUE, function will create a heatmap as well as return a matrix of 1s and 0s
`title`	Title of the heatmap

Value

Heatmap

Author(s)

Ahmer Jamil engr.ahmerjamil@gmail.com

Examples

healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")
healthy = methAlign(healthy,reference)
hHeatmap = methHeatmap(healthy,plot=TRUE)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MethTargetedNGS)
Loading required package: stringr
Loading required package: seqinr
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    space

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    translate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MethTargetedNGS/methHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: methHeatmap
> ### Title: Generate Heatmap of the given methylation data.
> ### Aliases: methHeatmap
> ### Keywords: Heatmap Methylation
> 
> ### ** Examples
> 
> healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
> reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")
> healthy = methAlign(healthy,reference)
Time difference of 1.9 secs
> hHeatmap = methHeatmap(healthy,plot=TRUE)
Percentage Result is 99.71> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>