POLYFUN_import_priors: Import pre-computed priors

In RajLabMSSM/echofinemap: echoverse module: Fine-mapping functions

Import pre-computed priors

Description

Import SNP-wise prior probabilities pre-computed from many UK Biobank traits. This function handles finding the intersection of SNPS that exist in the input GWAS summary stats dat and the pre-computed priors that come shipped with PolyFun. Then, it saves this subset as a new file for PolyFun (or other fine-mapping tools) to use as input. Uses the extract_snpvar.py script from PolyFun.

Usage

POLYFUN_import_priors(
  locus_dir,
  dat = NULL,
  polyfun = NULL,
  force_new_priors = TRUE,
  remove_tmps = FALSE,
  nThread = 1,
  conda_env = "echoR_mini",
  verbose = TRUE
)

Source

https://www.nature.com/articles/s41588-020-00735-5

See Also

Other polyfun: POLYFUN_compute_priors(), POLYFUN_download_ref_files(), POLYFUN_find_folder(), POLYFUN_finemapper(), POLYFUN_gather_annotations(), POLYFUN_gather_ldscores(), POLYFUN_help(), POLYFUN_initialize(), POLYFUN_munge_summ_stats(), POLYFUN_prepare_snp_input(), POLYFUN_run_ldsc(), POLYFUN()

RajLabMSSM/echofinemap documentation built on Jan. 3, 2023, 1:42 a.m.