A Fast and Light Package to Compute Polygenic Risk Scores

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Documentation for package ‘RapidoPGS’ version 2.3.0

• 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