My main question: Are there packages in R that I can use to compare copy number variation (CNV) between two populations?
Background:
I am a student and new to bioinformatics/statistics. I am interested in variation of a class of simple sequence repeats/microsattelites/ Tandem repeats (whatever you want to call them) and used a tool to determine their copy numbers in WGS data from a population of humans and a population of rhesus macaques.
I have the copy numbers in R as a dataframe with loci as rows and individuals as columns, looking something like this:
Most loci have the same copy number across all individuals (true for both populations), but I want to find the few that are variable. (In this data, copy number can only be a discrete value/integer).
I would also like to know which loci are the most variable in one population (have the most number of alternative copy numbers or another measure of variation) and which ones are more or less variable when comparing both populations.
Lastly, I want to know which loci are significantly higher or lower in copy number between the populations.
How can I tackle this? Is there a package or specific statistic test I can use to do something like this?
Ideally I would want to use something like the DESeq package but more tailored for copy number data, (though I suspect there to be not that many suitable packages as well thought out as DESeq)
Any recommendations/comments are welcome, cheers!
