Create metadata table

[adilahiri]

Purpose/implementation Section

What scientific question is your analysis addressing?

Create Table S1 for future manuscript to contain the histologies file along with a README

What was your approach?

Adapted code from:
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/tables/output_tables.Rmd

What GitHub issue does your pull request address?

Issue#459

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

Which areas should receive a particularly close look?

Please review TableS1-histologies.xlsx and the script output_tables.nb.html

Is there anything that you want to discuss further?

NA

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)?

Table

What is your summary of the results?

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

• [ X] 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.
• [ X] The analytical code is documented and contains comments.

[jharenza]

Hi @adilahiri thanks for starting this. Can you make sure all columns from v11 are represented in the readme? Eg - the methylation information. Thanks!

[adilahiri]

@jharenza thank you for pointing out the missing methylation columns. I have added them into the README now.

Following are the extra columns that have been added to README. I have added the description based on my understanding, but they can be improved especially for the classification scores by specifying the type of score (accuracy, F-1, roc_auc_score etc).

Histology column	Definition
cns_methylation_class	methylation-based CNS tumour classes
cns_methylation_class_score	class score
cns_methylation_subclass	methylation-based CNS tumour sub-classes
cns_methylation_subclass_score	subclass score
gtex_group	Tissue Type
gtex_subgroup	Tissue Subtype
RF_purity_ABSOLUTE	purity score based on ABSOLUTE dataset
RF_purity_ESTIMATE	purity score based on ESTIMATE dataset
RF_purity_LUMP	purity score based on LUMP dataset

[jharenza]

few comments, I will commit, rerun, and approve this so we can hand off to NCI

[jharenza]

I will merge this without checks since it doesn't run in GA