Updated deep loss CNV calls

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Add logic for a "deep loss" call for focal CN output files.

What was your approach?

Changed:

OpenPBTA-analysis/analyses/focal-cn-file-preparation/04-prepare-cn-file.R

Lines 240 to 247 in 6bf301e

	# Merge and annotated no X&Y
	autosome_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_no_xy,
	txdb_exons = tx_exons) %>%
	# mark possible amplifications in autosomes
	dplyr::mutate(status = dplyr::case_when(
	copy_number > (2 * ploidy) ~ "amplification",
	TRUE ~ status
	))

To:

# Merge and annotated no X&Y
autosome_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_no_xy,
                                                   txdb_exons = tx_exons) %>%
  # mark possible amplifications and deep loss in autosomes
  dplyr::mutate(status = dplyr::case_when(
    copy_number > (2 * ploidy) ~ "amplification",
    copy_number == 0 ~ "deep loss",
    TRUE ~ status
  ))

Changed:

OpenPBTA-analysis/analyses/focal-cn-file-preparation/04-prepare-cn-file.R

Lines 265 to 267 in 6bf301e

	# Merge and annotated no X&Y
	sex_chrom_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_sex_chrom,
	txdb_exons = tx_exons)

To:

  sex_chrom_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_sex_chrom,
                                                      txdb_exons = tx_exons) %>%
  # mark possible deep loss in sex chromosome
  dplyr::mutate(status = case_when(
    copy_number == 0  ~ "deep loss",
   TRUE ~ status
  ))

What GitHub issue does your pull request address?

#1099

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

• Please verify in the conditions for "deep loss" seem right to you.
• The chromosome arm and cytoband level copy_number annotation uses only "gain" and "loss" as status; amplification is converted to gain
  Should we convert the "deep loss" added in this PR as "loss" for cytoband annotation OR do we want to add amplification and deep loss annotation to cytobands?

Is there anything that you want to discuss further?

NA

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

table

What is your summary of the results?

"Deep loss" calls were added to focal CN files for autosomes and X+Y calls.

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[kgaonkar6]

@jharenza
I’ve now updated the CN==0 as the only criteria for “deep loss”

The chromosome arm and cytoband level copy_number annotation uses only "gain" and "loss" as status; amplification is converted to gain
Should we convert the "deep loss" added in this PR as "loss" for cytoband annotation OR do we want to add amplification and deep loss annotation to cytobands?

Does this sound ok as is ?

XY chromosomes don’t have a logic in the current code y to add applications does that sound ok too?

[jharenza]

This looks good, just want to switch the nomenclature to deep deletion

[kgaonkar6]

Thanks for the review @jharenza 🙌. I'll rerun and commit the updated nomenclature output

[jharenza]

see comment about removing the amp-->gain change in XY seg file

disregard this - we can make this an after #1048 issue