Updated analysis: medulloblastoma consensus subtypes

[jharenza]

What analysis module should be updated and why?

#742 via #738 #743

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

Will need to be updated once #746 goes in

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

RNA-Seq collapsed tables
File to be released in #746

When do you expect the revised analysis will be completed?

unsure

Who will complete the updated analysis?

probably @komalsrathi

[komalsrathi]

@jharenza I think it should be PR #743 instead of #738. That's where I am using the expected subtypes to compare the classifiers with the pathology report.

[jharenza]

@jharenza I think it should be PR #743 instead of #738. That's where I am using the expected subtypes to compare the classifiers with the pathology report.

updated, thanks!

[jharenza]

@komalsrathi - will you use the new file below as input for the classifier accuracy assessment? Thank you!

openPBTA-mb-pathology-subtypes.csv

[komalsrathi]

@jharenza can you assign this to me? I never see these tickets unless they are assigned (only get notified and then I have to search for it).

[jharenza]

@jharenza can you assign this to me? I never see these tickets unless they are assigned (only get notified and then I have to search for it).

done!

[komalsrathi]

@komalsrathi - will you use the new file below as input for the classifier accuracy assessment? Thank you!

openPBTA-mb-pathology-subtypes.csv

@jharenza This file does not contain two columns that we have in the current input file:
Kids_First_Biospecimen_ID and other_molecular_findings. These are also added in the output files. We don't necessarily need the other_molecular_findings field I think but BS id is required to map the output of classifier (which uses expression data and hence the BS ids) to this file. If you can update the csv file, it would be easy to incorporate. I don't want to make any local changes to this file on my end as I am seeing this was referenced in other tickets as well. Thanks!

This is the input file for ref: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/molecular-subtyping-MB/input/expected_class_v17.rds

So you can also either write it out as an rds (along with the version) or I can do that on my end.

[jharenza]

Added BS_ID but removed other_molecular_findings to keep this lite for the release.
openPBTA-mb-pathology-subtypes.csv

[jharenza]

Closed with #1019