Updated analysis: HGG fusion steps

[jaclyn-taroni]

What analysis module should be updated and why?

molecular-subtyping-HGG uses fusion data, which is cleaned in analyses/molecular-subtyping-HGG/05-HGG-molecular-subtyping-fusion.Rmd. The putative oncogenic fusion file is being updated as part of v15.

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

Unclear if we now have FGFR1--TACC1 in the putative oncogenic fusion file now:

OpenPBTA-analysis/analyses/molecular-subtyping-HGG/05-HGG-molecular-subtyping-fusion.Rmd

Line 124 in 286ff25

"FGFR1--TACC1",

We also need to generate new subset files with analyses/molecular-subtyping-HGG/02-HGG-molecular-subtyping-subset-files.R and everything downstream of the 05 fusion notebook and check for any change in interpretation/update notebook documentation.

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

v14

When do you expect the revised analysis will be completed?

Around the same time as #574. ~1 day barring any unforeseen complications.

Who will complete the updated analysis?

Likely someone from the CCDL.

[jaclyn-taroni]

New subset files from v15 were generated as part of fixing v15 breaking changes (#586) where the entire module was rerun. I have revisited the fusions notebook (analyses/molecular-subtyping-HGG/05-HGG-molecular-subtyping-fusion.Rmd) and we don't see any additional FGFR1-- fusions and therefore none of the interpretations change. I am closing this issue.