Pilot studies

Site map

• Pilot (N=196)
  • data/ contains genotype files in .bgen format
  • bgen/ PLINK2 results according to .bgen files; summary outputs and sentinels/ directory are in the following directories
    • 1e-5
    • 1e-6
    • 5e-8
• Batch 2 (N=1,488)
  • data2/ contains genotype files in .bgen format
  • bgen2/ PLINK2 results according to .bgen files; summary outputs and sentinels/ directory are in the following directories
    • 1e-5
    • 5e-8
  • Comparison of pilot and batch 2
    • miamiplot
• Batch 3 data (N=807)
  • data3/ .bgen data
  • bgen3/ PLINK2 results
    • 1e-5
    • 5e-8

Coding

There are apparent commonalities between batches from the list of programs and diagrams; many of which are activated as subroutines.

• Pilot
  • caprion.R and caprion.ini are for data processing. Their derivatives are in the utils/ subdirectory:
    • affymetrix.sh is for variant-specific association analysis.
    • qctool.sb is used to extract available sample and genotypes.
    • qctool.sh further extracts genotypes with MAF 0.01 only.
    • plink2.sh non-SLURM version of association analysis.
    • qqman.sh and qqman.R produce QQ and Manhattan plots.
    • sentinels_nold.sh and merge.sh select sentinels.
    • ps.sh and ps.R run through PhenoScanner.
    • lookup.sh looks up for overlap with SomaLogic and Olink.
    • caprion.ipynb is a Jupyter notebook with some preprocessing done by tensorqtl.sh.
• Batch 2 (prefix=utils/ when unspecified)

• Batch 3 (prefix=utils/)

Note that eSet.R actually covers data from pilot, batches 2 and 3.

Documents

• ppr.md
• EPCR-PROC.md
• 2021.md

Reference

Klaus B, Reisenauer S (2018). An end to end workflow for differential gene expression using Affymetrix microarrays.

https://bioinformatics.psb.ugent.be/webtools/Venn/