Question: How to plot curves of the distance correlation between the methylation status of neighbouring CpG sites..??
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gravatar for vsivaranjanipriya
5.1 years ago by
vsivaranjanipriya30 wrote:

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..

sequencing next-gen • 1.8k views
ADD COMMENTlink written 5.1 years ago by vsivaranjanipriya30

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.

ADD REPLYlink written 5.1 years ago by Devon Ryan92k

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

ADD REPLYlink written 5.1 years ago by Devon Ryan92k

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

ADD REPLYlink written 5.1 years ago by vsivaranjanipriya30

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).

ADD REPLYlink written 5.1 years ago by Devon Ryan92k
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