computePGS |
Compute PGS from GWAS summary statistics using posteriors from Wakefield's approximate Bayes Factors |
EUR_ld.blocks |
LD block architecture for European populations (hg19). |
EUR_ld.blocks38 |
LD block architecture for European populations (hg38). |
gwascat.download |
Retrieve GWAS summary datasets from GWAS catalog "gwascat.download' takes a PMID from the user and downloads the associated summary statistics datasets published in GWAS catalog |
logsum |
Helper function to sum logs without loss of precision |
michailidou |
Subset of Michailidou BRCA GWAS sumstat dataset. |
sdY.est |
Estimate trait variance, internal function |
wakefield_pp |
compute posterior probabilities using Wakefield's approximate Bayes Factors 'wakefield_pp' computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant. |
wakefield_pp_quant |
Compute posterior probabilities using Wakefield's approximate Bayes Factors for quantitative traits |