Grouping Cnv After Segmentation Using Bioconductor Dnacopy

Question

[Mdeng]

Hey everyone,

I got some nice hints here. And of course in the resulting output I get informations about the CNV. But, what I am asking myself: can group this? Are there thresholds, which I could apply, to distinguish between gain, loss and neutral? And: What are the 3rd and the 4th values? Is the 4th a ratio?

With best,

Mario

P.S. Here are the first lines of the output

chr1    721289  721497  209     -0.888
chr1    753325  753413  89      -0.561
chr1    808650  808847  198     -0.609
chr1    808853  808949  97      -0.647
chr1    808950  809012  63      -0.155
chr1    809013  809028  16      -0.450
chr1    809096  809258  163     -0.515
chr1    809343  809531  189     -1.254
chr1    809537  809562  26      -0.046
chr1    809563  809651  89      -0.800
chr1    809652  809722  71      -0.321
chr1    809723  809800  78      -0.447
chr1    809801  809854  54      -0.076

Answer 1

[Chris Miller]

The columns should be chr, start, stop, # of windows in that segment, and the log2 copy number at that segment.

There's no hard and fast rule on how to set these thresholds, unless you've got some spike-in data and can approximate levels that will give you high sensitivity and a low false positive rate. Some reasonable thresholds for your usage might be log2(3/2) = 0.5849625 for gain and log2(1/2) = -1 for loss (equivalent to CN > 2.5 and CN < 1.5)

[Mdeng]

Thanks for the hint. Just got the wrong lines in the clipboard. Corrected it.

[Sean Davis]

@Chris, equivalent to CN > 3 and CN < 1, respectively, on the last line?