POLYFUN_prepare_snp_input: Prepare SNP input for PolyFun

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

Prepare SNP input for PolyFun

Description

PolyFun requires a space-delimited (gzipped or not) file with these columns:

• CHR

• BP

• A1

• A2

Usage

POLYFUN_prepare_snp_input(PF.output.path, locus_dir, dat = NULL, nThread = 1)

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_import_priors(), POLYFUN_initialize(), POLYFUN_munge_summ_stats(), POLYFUN_run_ldsc(), POLYFUN()

Examples

BST1 <- echodata::BST1; locus_dir <- echodata::locus_dir;
dat <- BST1
PF.output.path <- file.path(locus_dir, "PolyFun")
POLYFUN_prepare_snp_input(PF.output.path=PF.output.path, locus_dir=locus_dir, dat=dat)

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