Updated analysis: fusion summary to add fusions for LGG

[jharenza]

What analysis module should be updated and why?

fusion summary
Currently, the LGAT subtyping module only looks for BRAF fusions, so it utilizes the pbta-fusion-putative-oncogenic.tsv file directly. Since we are adding many more subtypes and considering additional fusions, we should create a new fusion summary file containing this information.

OpenPBTA-analysis/analyses/molecular-subtyping-LGAT/02-make-lgat-final-table.Rmd

Lines 54 to 60 in 793c604

	brafFusion <- readr::read_tsv(file.path(data_dir,
	"pbta-fusion-putative-oncogenic.tsv")) %>%
	select(Sample, FusionName) %>%
	distinct() %>%
	filter(grepl("BRAF", FusionName),
	Sample %in% lgat_rnaseq_bsids) %>%
	rename(Kids_First_Biospecimen_ID = Sample)

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

Create and add fusion_summary_lgg_foi.tsv file consisting of the following fusions and genes with fusions:

Fusions:
KIAA1549--BRAF
FGFR1-TACC1
MYB-QKI

Genes with fusions:
BRAF
ALK
ROS1
NTRK1
NTRK2
NTRK3
PDGFRA
FGFR2
FGFR1
MYB
MYBL1
RAF1

For kinase fusions with a 5' kinase, we should use an adaptation of #665 to confirm likely functionality and if these conditions are satisfied, then we will add those fusions to the final file:
1. Is reciprocal == yes
2. Kinase domain retained == yes
3. inframe == yes

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

pbta-fusion-putative-oncogenic.tsv

When do you expect the revised analysis will be completed?

2-3 days

Who will complete the updated analysis?

@kgaonkar6

[jharenza]

@kgaonkar6, I will work on this once #821 is merged

[jharenza]

closed with #830