Feature request: tidy save L2R Baf and gene tables

[apastore]

Hi one more question, would be possible to export ( eventually in one result project folder) all the seg file, gene tables L2R and BAF tables? Also ASCAT and FACET ploidy and cellularity predictions?

Thanks!
Alessandro

[aoumess]

For each sample, all these info are actually exported in the corresponding sample subfolder.
If you mean exporting an aggregation of such data in a single object / table for a cohort of samples, it is planned on my to-do list when I'll add a cohort object to EaCoN. The next planed step being performing cohort analyses such as sub-groups differential analysis, clustering (hierarchical, skmeans, NMF), paired analysis, etc... All codes are already there but need some shaping. Please just be patient, this will be added in a few releases ;)

[apastore]

Thanks for your clarification !Perfect! Maybe could you also export a cohort wise purity and ploidy table ? This would be really nice, since Is not immediately clear with model ASCAT select. Thanks a lot!

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On Jan 21, 2019, at 9:19 AM, Bastien Job ***@***.***> wrote: For each sample, all these info are actually exported in the corresponding sample subfolder. If you mean exporting an aggregation of such data in a single object / table for a cohort of samples, it is planned on my to-do list when I'll add a cohort object to EaCoN. The next planed step being performing cohort analyses such as sub-groups differential analysis, clustering (hierarchical, skmeans, NMF), paired analysis, etc... All codes are already there but need some shaping. Please just be patient, this will be added in a few releases ;) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[kunstner]

Hi @aoumess,
thanks for this wonderful package. However, I was wondering whether you made some progress on implementing the cohort feature. I have a rather big cohort where I would like to use EaCoN for the final analyses as well.
Best,
Axel

[aoumess]

@kunstner : Better late than never, I'm currently writing it. It will probably be an independent package named 'EaCoNiC' (Easy Copy Number in Cohort). Actually, the aggregation step of L2R & BAF segmentation results is done. Now, I'm migrating / rewriting some old code segments to add differential analysis (wilcoxon / kruskal-wallis -based), sample clustering (hierarchical, km/pam, and NMF), auto-correlation (genomic regions that are simultaneously aberrant, or inverted), and data processing to create input files to GISTIC 2. These items will be implemented step by step, in that said order.