Hello!
I would like to retrieve data from copy number variants for all cell lines. The most important information for me is the absolute copy number of minor and major alleles for a given segment. I found such a file in the current release (OmicsAbsoluteCNSegmentsProfile.csv), but unfortunately after downloading it I get a different file. The difference is not big - instead of the MajorAlleAbsoluteCN column there is a SegmentAbslouteCN column.
Of course, I should be able to calculate the absolute number of major alleles, but there are a lot of floating point values in SegmentAbsolutreCN and I’m not sure how to interpret them.
Moreover, in the second file named OmicsCNSegmentsProfile.csv there is a completely different number of variants and not all of them correspond to the first file.
Is this some kind of error in the files?
Thank you for any help!
The column name SegmentAbslouteCN in OmicsAbsoluteCNSegmentsProfile.csv is correctly indicating the total CN (major + minor). We are aware that the file description states that it includes “MajorAlleleAbsoluteCN”, which is a typo that will be fixed soon in the upcoming DepMap release.
The floating points in OmicsAbsoluteCNSegmentsProfile are most likely noise and should be ignored.
On the other hand, OmicsCNSegmentsProfile.csv is relative copy number instead of absolute, generated using a completely different algorithm. They are meant to be different despite similar file names.
The floating point values happen both in case of high CN values (where, ignoring decimal part seems to be a sensible approach), but also in the range between 0 and 1.
I am wondering how to interpret values such as 0.47 or 0.61? They occur not only for short segments, here an example for a segment with a length of almost 2.5 Mb:
Would you recommend rounding them or ignoring the region as undetermined?
