V20 CNV update part2: focal cnv and oncoprint rerun

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Just a rerun for focal-cn and oncoprint after #1123

What was your approach?

I added the conditions to use base histology in focal-cn-preparation module to run for subtyping when needed.

What GitHub issue does your pull request address?

#1125

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

Which areas should receive a particularly close look?

NA

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)?

tables

What is your summary of the results?

Rerun of focal calls and oncoprint from updated overlap #1123

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.

[jharenza]

The majority of the goi oncoprints did not change. ATRX deletion was recovered in two HGAT samples, one of which is annotated on pedcbio and we had been missing previously: https://pedcbioportal.kidsfirstdrc.org/patient?studyId=pbta_all&caseId=PT_7WT6P5M8

This looks good to me.

[kgaonkar6]

Also wanted to add here that all updates in status in this update were NA in previous CNV calls.
change_log.txt

> change_log %>% select(status_latest,status_previous) %>% replace_na(list(status_latest="NA",status_previous="NA")) %>% table()
               status_previous
status_latest   amplification gain loss  NA
  amplification            10    0    0   3
  gain                      0  370    0  58
  loss                      0    0  126  43

[jaclyn-taroni]

If this fixes #1129, I will close #1130

[jaclyn-taroni]

Merging based on @jharenza 's review!