#790 Part2: adding Fusion based subtyping for LGAT

[kgaonkar6]

⚠️ #842 needs to be merged before this PR, 02-subset-fusion-files-LGAT.R and output can be reviewed independently though

Purpose/implementation Section

LGAT subtyping is being revamped as per issue. I'm diving into this with staggered PRs per alteration as:

• SNV #790 Part1: adding new SNV subtypes for LGAT #842
• Fusion #790 Part2: adding Fusion based subtyping for LGAT #843
• CNV #790 Part3: adding CNV based subtyping for LGAT  #845

What scientific question is your analysis addressing?

As per issue we will be subtyping LGAT based on fusion in the following genes:

• LGG, KIAA1549-BRAF
  contains KIAA1549-BRAF fusion

• LGG, other MAPK
  contains non-canonical BRAF fusion other than KIAA1549-BRAF
  contains RAF1 fusion

• LGG, RTK
  harbors a fusion in ALK, ROS1, NTRK1, NTRK2, or NTRK3 or
  harbors a PDGFRA fusion

• LGG, FGFR
  harbors FGFR1-TACC1 fusion
  harbors FGFR1 or FGFR2 fusions

• LGG, MYB/MYBL1
  harbors either a MYB-QKI fusion or other MYB or MYBL1 fusion

What was your approach?

• I used a list of genes to look for in presence of fusion or fused genes per subtype.
• I'm using file from lgat fusion-summary , add fusion summary for LGAT #830 checks for kinase overlap and reciprocal fusion for LGAT biospecimen fusions.

The fusion status per subtype is saved as lgat-subset/LGAT_fusion_subset.tsv

	Kids_First_Biospecimen_ID	KIAA_BRAF_fus	MAPK_fus	RTK_fus	FGFR_fus	MYB_fus

What GitHub issue does your pull request address?

#790

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

Which areas should receive a particularly close look?

We will have to review/push through #842 since SNV subtyping was done in the previous PR.

Is there anything that you want to discuss further?

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)?

lgat-subset/LGAT_fusion_subset.tsv

What is your summary of the results?

122 biospecimens have canonical KIAA1549--BRAF, 12 biospecimens have fusion in other MAPK genes, 14 biospecimen have fusions in RTK genes, 3 biospecimens have MYB fusion.
There are no FGFR1--TACC1 or FGFR fusion in the lgat biospecimen list.

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]

Closing this because unwanted tp53-classifier-score files got added to this PR