Calculate Methylation Average of given methylation matrix

Description

Methylation average of a CpG site is the percentage of unmethylated cytosine or methylated cytosine in a particular CpG site. The methylation average of a particular CpG site was calculated by number of cytosine divided by sum of total number of methylated and unmethylated cytosine at particular CpG site in a group of reads.

average = NC/(NC + NT)

Usage

methAvg(Sample, plot = FALSE)

Arguments

Value

Vector containing average methylation of given methylation matrix. Length of the vector represents the number of CpG sites in methylation matrix.

Author(s)

Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri

Maintainer: Muhammad Ahmer Jamil engr.ahmerjamil@gmail.com

See Also

methAlign, compare_samples

Examples

healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")
methP <- methAlign(healthy,reference)
avgMeth <- methAvg(methP,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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> 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/methAvg.Rd_%03d_medium.png", width=480, height=480)
> ### Name: methAvg
> ### Title: Calculate Methylation Average of given methylation matrix
> ### Aliases: methAvg
> ### Keywords: Average Methylation
> 
> ### ** Examples
> 
> healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
> reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")
> methP <- methAlign(healthy,reference)
Time difference of 2.11 secs
> avgMeth <- methAvg(methP,plot=TRUE)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>