Question: Ploidy Analysis in R
0
gravatar for gargar
19 months ago by
gargar0
gargar0 wrote:

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,

snp methylation ploidy R 450k • 723 views
ADD COMMENTlink modified 19 months ago by Kevin Blighe48k • written 19 months ago by gargar0
1
gravatar for Kevin Blighe
19 months ago by
Kevin Blighe48k
Kevin Blighe48k wrote:

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 I did this previously (unpublished) but based on NGS depth of coverage profiles.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.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Kevin Blighe48k

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.

ADD REPLYlink written 18 months ago by Ezhil La10

Yes, if you have segment data, you can feed this into ABSOLUTE: http://archive.broadinstitute.org/cancer/cga/absolute_run

ADD REPLYlink written 18 months ago by Kevin Blighe48k
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