Add spatiotemporal SETBP1 target permutation analysis

[lizzyjoan]

Summary

This is a permutation analysis using SETBP1 target genes in BrainSpan developmental brain data (prenatal and postnatal) and adult and developmental GTEx data (postnatal, tissues related to SETBP1 disorder phenotypes). I also calculate target coexpression with SETBP1 across datasets and include a plotting script.

This analysis should be reflected in the current manuscript draft under "SETBP1 target spatiotemporal permutation testing" Methods section and "Spatio-Temporal Expression and Functional Prioritization Identifies Key Neurodevelopmental Targets of SETBP1" Results section.

Author Checklist

• This repository has a Lasseigne Lab ruleset configured.
  See instructions here.
• A singularity container has been created with all dependancies and the
  cap_container command has been included in each script using a container.
• All of the necessary scripts, dependencies, and inputs have been included
  in this pull request.
• Only files relevant to this change are included; no temporary, generated,
  or unrelated files are part of this pull request. Use .gitignore to prevent
  irrelevant files from accidentally being included.
• Results have been reproduced and verified with lasseignelab and
  default environments by running the job until two consecutive runs produce
  the same results. Code comments (per script) have been added for
  non-reproducible scripts. Include information about why the script is not
  reproducible.
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Self/Peer Review Checklist (Coding Guidelines)

• Meaningful variable and function names
• File header comments
• Function comments
• In-line comments summarize logical sections of code by concisely explaining
  why, not what the code is doing. Avoid excessive or redundant commenting.
• Random seed is set
• Reasonable processing time for each job or script is specified
• All outputs have been saved
• Session info included in the scripts
• Cross-reference the working draft of the paper
• Confirm the code performs the intended analysis
• Confirm the code reproduces the reported results

Setup

Ensure you have CAPTURE v1.0.0 with the cap version and cap update commands.

cd $USER_SCRATCH/setbp1_hd
git checkout main
git pull

git checkout permutation
git pull origin permutation

Reproduce results

Download Brainspan and GTEx data
Should take < 10 minutes

cap run -s batch -e default src/permutation_analysis/01_fetch_temporal_exp.sh

Brainspan and GTEx permutation analyses should each take ~30-55 minutes

cap run -s batch src/permutation_analysis/02_job_permutation.sh
cap run -s batch src/permutation_analysis/03_job_permutation.sh

Once permutation scripts have completed, run plotting script.
Plotting script should take < 5 minutes

cap run -s batch src/figures/01_supp_figure.sh

Verification

cap verify -s batch verifications/permutations_fetchdata.sh
cap verify -s batch verifications/permutations_run.sh

Then check for any differences

git diff verifications/

This should return nothing, indicating no differences between outputs

Cleanup and Symlink

Only run this after verifying outputs!!
This will remove your specific download of BrainSpan and GTEx data, and instead symlink to the Lasseigne Lab DATASET_dir

rm -rf data/brainspan
rm -rf data/gtex
cap run -s batch -e lasseignelab src/permutation_analysis/01_fetch_temporal_exp.sh -n

ls -hal data/

The gtex/developmental, gtex/adult, and brainspan directories should point to the Lasseigne Lab DATASET_dir on Cheaha.

[tsoelter]

Looks like I am missing the updated setbp1 targets CSV file 260403_setbp1_targets.csv, so the 02 and 03 jobs in this PR fail.

[lizzyjoan]

Looks like I am missing the updated setbp1 targets CSV file 260403_setbp1_targets.csv, so the 02 and 03 jobs in this PR fail.

Sorry, thought for sure I'd added and mistook the old file for the new one (with the names so close!) this should be fixed now!

[tsoelter]

Scripts run and verify! 🎉 I left a few additional comments regarding typos, potential dead code, and some minor issues during filtering and file writing.

[lizzyjoan]

Scripts run and verify! 🎉 I left a few additional comments regarding typos, potential dead code, and some minor issues during filtering and file writing.

I believe I've addressed all your comments

[sashataluri]

I reviewed and ran this pull request. I also verified our results.

Looks good.

[tsoelter]

Changes look good and everything still verifies! 🎉