Description Usage Arguments Value Author(s) See Also Examples

View source: R/sequenceAlignment.R

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)

1 |

`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 [email protected]

1 2 3 4 | ```
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)
``` |

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