Clarify docs on GISTIC export

[lbeltrame]

As it's still quite used, it would be nice to provide an example on how to generate a GISTIC compatible output from a segment table. It took a while for me, and required trial and error runs with GISTIC.

[fredcommo]

Your are right, even though I think it's more on GISTIC users to be aware
of what data format is required to run this program.
GISTIC also provides a lot of information and demo files. Looking at these
example files can be a good starting point :)

2016-06-10 11:41 GMT+02:00 Luca Beltrame notifications@github.com:

As it's still quite used, it would be nice to provide an example on how to
generate a GISTIC compatible output from a segment table. It took a while
for me, and required trial and error runs with GISTIC.

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[lbeltrame]

The problem is that the GISTIC docs are pretty lacking, at least for someone not into the world of CNA/CNV. What I understood now is that to produce their seg.cn one would need to use the log2ratio -1 (where 1 is the diploid value). I've tried both with seg.mean and estimCopy, but only the latter seems to make GISTIC not break.

That is why there is the need for some clarification.