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