cgMethFinder: Methylation status

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

Value

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.

Examples

Run this code

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

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