methAvg {MethTargetedNGS} | R Documentation |
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)
methAvg(Sample, plot = FALSE)
Sample |
Matrix from methAlign. Also matrix where columns represents Cytosine of CpG sites and rows represents sequences. |
plot |
Boolean. TRUE if need a plot after calculation. Default FALSE |
Vector containing average methylation of given methylation matrix. Length of the vector represents the number of CpG sites in methylation matrix.
Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri
Maintainer: Muhammad Ahmer Jamil engr.ahmerjamil@gmail.com
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)