update EPN fusion gene `MAML2` in fusion summary module - Githubissues

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

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update EPN fusion gene `MAML2` in fusion summary module #1619

Closed jharenza closed 1 year ago

jharenza commented 1 year ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Fusion summary was mistakenly searching for the wrong EPN fusion for YAP1 subtype

What was your approach?

Update fusion summary to recode YAP1-MAMLD2 --> YAP1--MAML2

What GitHub issue does your pull request address?

Requirement for #1618

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

Which areas should receive a particularly close look?

Note: the header shifted

Is there anything that you want to discuss further?

No

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)?

What is your summary of the results?

4 bs_ids with YAP1--MAML2 fusion:

> epn %>%
+   filter(`YAP1--MAML2` == 1) %>%
+   pull(Kids_First_Biospecimen_ID)
[1] "BS_QP6MSKRE" "BS_WYERXS4G" "BS_1J2WQ08M" "BS_3DCBDJAT"

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.