cgMethFinder: Methylation status

In methVisual: Methods for visualization and statistics on DNA methylation data

Description

CpGs methylation status on clone sequence

Usage

cgMethFinder(ref,str)

Arguments

ref	String, genomic sequence, see selectRefSeq()
str	String, Single sequence under study after alignment to ref

Details

The function determines the methylation status of each CpG site by comparing TpG and CpG sites within the clone sequence to corresponding CpG sites in the reference sequence. The input values are the reference sequence and one of the clone sequences which is explored. It returns a (0,1) vector. 1 stands for methylated and 0 for non methylated state. This function is used in the methVisual package as internal function for the calculation of the methylation profiles.

Value

Returns a (0,1) vector. 1 stands for methylation and 0 for non methylation status.

Author(s)

Arie Zackay <[e-mail]>, ,Christine Steinhoff <[e-mail]>

Examples

ref <- "TTCGGGATCGTTTTTTTAGTAGGTCGGAAGTTTCGTTATGGATTCGTTTTTC"
str <- "TTCGGGATCGTTTTTTTAGTAGGTTGGAAGTTTTGTTATGGATTCGTTTTTC"
cgMethFinder(ref,str)

methVisual documentation built on April 28, 2020, 7:08 p.m.