tables and script added

[runjin326]

Purpose/implementation Section

What scientific question is your analysis addressing?

Output analysis results as tsv or excel file.

What was your approach?

Read in relevant files and output as tsv or excel.

What GitHub issue does your pull request address?

1187

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

Which areas should receive a particularly close look?

• For Table S2: 1) chromothripsis results table - I renamed column Kids_First_Biospecimen_ID column to Tumor_Sample_Barcode to be consistent with the rest of 4 tables 2) I also name each sheet - please review the names and I can change the names if needed
• For Table S3: 1) Just to confirm, for tab 2, for polya we use count results and for stranded we use FPKM results? 2) I also renamed column SampleID in tab2 to Kids_First_Biospecimen_ID_DNA to be consistent with the naming in TP53 scores tab but I can change if needed as well.

Is there anything that you want to discuss further?

Do we need a README file for this?

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)?

OpenPBTA_histologies_v21.xlsx   
tableS2_DNA_results_table.xlsx
tableS3_RNA_results_table.xlsx
subtypes-n.tsv          

I can change table names as well if needed.

What is your summary of the results?

The results are as expected.

Reproducibility Checklist

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

[runjin326]

@jharenza, I have now modified the scripts accordingly and added a README file. :)

[runjin326]

@jharenza, thanks for reviewing - I have made the suggested changes now.

[jharenza]

@runjin326 - I forgot that with https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1206 going in, we will have an update to a few WGS MB samples for molecular subtype. Can you update the histologies table to add these missed samples? These are To be classified, so it will not affect Table 1.

[runjin326]

@jharenza, I have now added the molecular subtype of those 7 samples in Table S1.