R: A Fast and Light Package to Compute Polygenic Risk Scores

# A Fast and Light Package to Compute Polygenic Risk Scores

## Documentation for package ‘RapidoPGS’ version 2.3.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

create_1000G | Download 1000 Genomes Phase III panel
EUR_ld.blocks19 | LD block architecture for European populations (hg19).
EUR_ld.blocks38 | LD block architecture for European populations (hg38).
find_file_in_ftp | Finding a file in an FTP directory This is an internal function to help 'gwascat.download' find the right file
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
michailidou19 | Subset of Michailidou BRCA GWAS sumstat dataset.
michailidou38 | Subset of Michailidou BRCA GWAS sumstat dataset.
rapidopgs_multi | Compute PGS from GWAS summary statistics using Bayesian sum of single-effect (SuSiE) linear regression using z scores
rapidopgs_single | Compute PGS from GWAS summary statistics using posteriors from Wakefield's approximate Bayes Factors
sd.prior.est | Compute Standard deviation prior (SD prior) for quantitative traits using pre-computed heritability.
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