Reference

All functions

EUR_ld.blocks19

LD block architecture for European populations (hg19).

EUR_ld.blocks38

LD block architecture for European populations (hg38).

create_1000G()

Download 1000 Genomes Phase III panel

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