Hi,
I don't know how to analyze the number of ploidy of aberrant genomes (q2n, q3n, q4n, etc) in Illumina 450K Infinium methylation data using R (I don't even know if it is possible).
Do you know how can I do it?
Thankyou,
This is certainly not a common task, hence, no comments or answers. However, a good starting point for you would be to build upon existing packages that can determine copy number from the 450K methylation array:
Once you identify global profiles of copy number, you can apply some extra customised steps to estimate ploidy. I did this previously (unpublished) but based on NGS depth of coverage profiles. It was surprisingly precise.
Edit: In fact, there appears to be a possible logical next step: If you derive global copy number segment profiles using one of the above-mentioned programs, then you could feed these into ABSOLUTE in order to detect ploidy.
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version 2.3.6
Hi Kevin,
I have global copy number segment profiles using conumee. From this, I would like to test whether the chromosome 1q is gained or lost. Could please suggest how to do this?
Many thanks.
Yes, if you have segment data, you can feed this into ABSOLUTE: http://archive.broadinstitute.org/cancer/cga/absolute_run
Hi Kevin, do you know of any literature regarding this workflow? Also, right now, only platforms ‘SNP_250K_STY’, 'SNP_6.0' and 'Illumina_WES' seem to be supported by ABSOLUTE. Which one would you choose for processing conumee data?
The conumee tutorial seems to be based on Illumina 450k data: http://bioconductor.org/packages/release/bioc/vignettes/conumee/inst/doc/conumee.html#perform-cnv-analysis
Can you adapt that to your own data?
Hey, thanks for your reply! I'm analyzing EPIC methylation data. The conumee data processing I've already done (so I have global segmented CN profiles), and now I'm curious if it would be possible to call absolute copy numbers (i.e. ploidy) on the conumee output. For that, I was thinking of using ABSOLUTE. But it seems that you have to choose a platform (‘SNP_250K_STY’, 'SNP_6.0' or 'Illumina_WES') in order to run the algorithm, so I'm not sure which to choose, since MethylationEPIC/conumee is not supported.