methHeatmap: Generate Heatmap of the given methylation data.

In MethTargetedNGS: Perform Methylation Analysis on Next Generation Sequencing 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 [e-mail]

See Also

methAlign

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)

Example output

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, 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:gplots':

    space

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:seqinr':

    translate

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

    strsplit

Time difference of 2.04 secs
Percentage Result is 99.71

MethTargetedNGS documentation built on Nov. 8, 2020, 8:10 p.m.