How to plot curves of the distance correlation between the methylation status of neighbouring CpG sites..??

Question

[vsivaranjanipriya]

Hi all.. I am doing MethylSeq data analysis.. As a part of analysis, I need to plot distance correlation curve for nearby CpG islands. Please guide me for the same...

This is a part of my output file from bismark,

Chromosome_no    start    end    methylation%
chr2    34532    34533    100
chr2    34540    34541    100
chr2    34562    34563    100
chr2    68432    68433    89.2
chr2    68448    68449    100
chr2    68456    68457    100
chr2    68460    68461    99.1568
chr2    127948    127949    100
chr2    176554    176555    100

Hoping for a sooner reply..

[Devon Ryan]

The biseq Bioconductor package has some functions for making variograms like this. That's not exactly what you want, but it'll give you some insight into how to code this in R.

[Devon Ryan]

Actually, it's probably easier to just use the acf() function in R.

[vsivaranjanipriya]

Thank You so much for your suggestions.. ll check it out..:)

[Devon Ryan]

Keep in mind that it defaults to assuming that the spacing between events is equal, so you'll have to find a way around that (or even just an autocorrelation function that simply allows unequal spacing between points).