Question: Comparing CNAs from two groups
1
gravatar for a.beggs
4.5 years ago by
a.beggs10
United Kingdom
a.beggs10 wrote:

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.

cnv cna • 1.0k views
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by a.beggs10

Thanks! Very useful.

ADD REPLYlink written 4.5 years ago by a.beggs10

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.

ADD REPLYlink written 4.5 years ago by Ryan D3.3k
3
gravatar for Istvan Albert
4.5 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

Bedtools has a new method called 'fisher' to test for statistical significance of overlaps http://bedtools.readthedocs.org/en/latest/content/history.html

ADD COMMENTlink written 4.5 years ago by Istvan Albert ♦♦ 79k
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