How to plot curves of the distance correlation between the methylation status of neighbouring CpG sites..??
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..
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vsivaranjanipriya •
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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.
Actually, it's probably easier to just use the
acf()function in R.Thank You so much for your suggestions.. ll check it out..:)
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).