Question: PLINK: enrichment analysis for CNV data
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gravatar for jurez
5.0 years ago by
jurez0
Slovenia
jurez0 wrote:

In PLINK 1.07 in rare CNV analysis section there is a module for enrichment analysis of CNV data. When I run the enrichment analysis (comparing weather a subset of genes are enriched, relative to all genes in hg19),  it produces three files: plink.log, plink.cnv.indiv and plink.cnv.burden. Despite some heavy searching I didn't find any documentation describing the plink.cnv.burden file. The file looks like this:

        TEST         BETA            P
        GCNT   0.00251894     0.505795
        NSEG   0.00371172     0.147517
       AVGKB  0.000513576    0.0409918

What is the meaning of the file? If I understand correctly, it reports the results of three tests: GCNT (what does this stands for?), NSEG(number of segmets), AVGKB (average kb). After reading the article by  Raychaudhuri et al, 2010, I am very cunfused, since the article mentions only single test, which takes into account many factors and should not solely rely on AVGKB or NSEG...

And what is BETA? Any help would be highly appreciated...

 

cnv plink enrichment • 1.5k views
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