Closed rjcorb closed 2 weeks ago
hi @rjcorb can you stack the MB PRs on https://github.com/d3b-center/OpenPedCan-analysis/pull/571? I had to remove MM2S code there.
@rjcorb can you do me a favor and label the following samples on the UMAP? These have very high-conf non-MB histologies and I wonder if these are some of the problematic samples. 7316-1884 7316-1676 7316-1666 7316-3202
Purpose/implementation Section
What scientific question is your analysis addressing?
Closes #569. This PR adds a script to
molecular-subtyping-MB/
to generate a UMAP of MB SHH samples based on most variable methylation array probes.What was your approach?
adapted from this code: https://jharenza.github.io/mb-subtypes/explore-medulloblastoma-unsupervised-clustering.nb.html
What GitHub issue does your pull request address?
569
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Check code and ensure script runs successfully:
R -e "rmarkdown::render('06-mb-shh-umap.Rmd')"
Is there anything that you want to discuss further?
I have the UMAP points sized by age range currently, to add some additional info on outliers and un-subtyped MB SHH samples. We may not want to keep this in the final figure.
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)?
UMAP
What is your summary of the results?
Overall we see good clustering of MB SHH samples into the four subtypes. There are a few samples not cluttering with their subtype, including a few adolescent/adult samples with the infantile MB SHH samples. We may need to review these samples to check how they were classified into subtypes.
Reproducibility Checklist
Documentation Checklist
README
and it is up to date.analyses/README.md
and the entry is up to date.