Comparing CNAs from two groups
Hi
I have a sample set with two groups, e.g. case vs. controls.
I have a list of CN calls for each sample but I want to aggregate them and pull out recurrent CNAs in the dataset, ideally with statistical significance
I thought about using multiIntersectBed but obviously this won't permit statistical testing.
I can't see any obvious packages searching through the usual sources.
Any suggestions gratefully received.
1 answer
Bedtools has a new method called 'fisher' to test for statistical significance of overlaps http://bedtools.readthedocs.org/en/latest/content/history.html
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Istvan Albert
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Thanks! Very useful.
Just curious if your CNAs all have identical breakpoints or not. What is the minor allele frequency threshold you are using? We typically examine only those CNVs with 5% MAF or higher.