Updated analysis: "more nuanced" copy number calls

[jaclyn-taroni]

Splitting up #486 into more focused tickets

What analysis module should be updated and why?

We broadly call copy number changes, i.e., we'll only label an event as a loss without considering whether the loss is homozygous or hemizygous or how many copies are lost (see A Note on Ploidy again) in the focal-cn-file-preparation steps for SEG files (CNVkit, consensus SEG). In the consensus case at least, we can potentially use the seg.mean values to guide us with any kind of thresholding - see this section of the notebook for processing the consensus SEG file: https://alexslemonade.github.io/OpenPBTA-analysis/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html#does_segmean_agree_with_status

What changes need to be made? Please provide enough detail for another participant to make the update.

Should we try to make more nuanced/detailed copy number calls using the (consensus) seg.mean values? From @jharenza on #182 (comment)

Note, this was also done using array data, not NGS, so we may have to figure out thresholds for cutoffs for accurate assessment of focal CN based on LRR (may advise starting with ATRT's and SMARCB1 deletions and we may not be able to do homozygous/hemizygous, but rather just deletions/amplifications - not sure - haven't dug into the data too much).

We could consider this in conjunction with the RNA-seq expression levels data (#387).

What input data should be used? Which data were used in the version being updated?

analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz / when pbta-cnv-consensus.seg.gz makes it to the data release

When do you expect the revised analysis will be completed? / Who will complete the updated analysis?

It is unclear if we would be able to accomplish this in a reasonable amount of time given the data that we have. It may be sufficient to document this potential limitation. I am hoping to discuss this in the CCDL team meeting this afternoon.