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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Update table 1 to remove duplicates & update ms tables to v22 #1462

Closed jashapiro closed 2 years ago

jashapiro commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

The Table 1 generation script was double counting some samples that had both WGS and RNA-seq specimens

What was your approach?

Added a distinct() step to count each sample_id only once.

Also updated to v22

What GitHub issue does your pull request address?

closes #1459

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

Which areas should receive a particularly close look?

The change to v22 and or rerunning the whole notebook resulted in a number of other changes. I have not checked these in detail to be sure that they are as expected, partly because they are all xls files, and partly because I am not sure I know all the expectations!

Is there anything that you want to discuss further?

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)?

New Tables for the manuscript.

What is your summary of the results?

Most of the counts in table 1 went down, as expected!

Reproducibility Checklist

Documentation Checklist

jharenza commented 2 years ago

@jashapiro I had #1448 started for rerunning of all tables with v22 release so that we could make sure some of the changes would come through as expected. I can close that one if want to keep this one open. However, note, that the full script will need to be rerun again once some other modules are updated (mut sigs, survival), since those results are included in tables.

jashapiro commented 2 years ago

@jashapiro I had #1448 started for rerunning of all tables with v22 release so that we could make sure some of the changes would come through as expected. I can close that one if want to keep this one open. However, note, that the full script will need to be rerun again once some other modules are updated (mut sigs, survival), since those results are included in tables.

Oh, I missed that, sorry! I'll just suggest the important change there!