R/~old/pipeline.md

In BaderLab/POPPATHR: Population-based pathway analysis of SNP-SNP coevolution

PopulationPathways workflow

1) recodeFAM.R

• recodes PLINK fam file to case/control format by population
• supports running phenotype-based permutations (see setupGSEArun.R)

2) popPCA.R

• performs cluster analysis (PCA) between both studied populations via PLINK --cluster
• outputs MDS plot (OPTIONAL)

3) SNP2gene.R

• integrates input SNP locations to their nearest gene
• code adapted from GWAS2pathway map_snp2gene.R (by Shraddha Pai)

4) calcFST.R

• calculates population-based differentiation in minor allele frequency (FST) via PLINK --fst case-control
• outputs GSEA input SNP statistics file (SNP-FST)

5) setupGSEArun.R

• calculates pathway enrichment statistics via gene-set enrichment analysis
• selection-enriched pathway: enriched for high-FST genes in one population compared to the other (i.e., enriched for positive selection)
• unenriched pathway: similar pathway-level FST between both populations (i.e., not enriched for positive selection)
• code adapted from GWAS2pathway GSEA_setup.R

6) getPathStats.R

• generates SNP and gene lists per 'enriched' and 'unenriched' pathway as determined by GSEA for downstream analysis

7) LDstatsWPM.R

• calculates extent and strength of coevolution within the pathways enriched for positive selection
• uses inter-chromosomal linkage disequilibrium (LD) as a proxy for SNP-SNP coevolution

7) LDstatsBPM.R

• calculates extent and strength of coevolution between pairs of pathways enriched for positive selection
• uses inter-chromosomal linkage disequilibrium (LD) as a proxy for SNP-SNP coevolution

BaderLab/POPPATHR documentation built on Dec. 17, 2021, 9:53 a.m.