A Fast and Light Package to Compute Polygenic Risk Scores


[Up] [Top]

Documentation for package ‘RapidoPGS’ version 1.0.2

Help Pages

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