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Prepare SNP input for PolyFun

Source: R/POLYFUN_prepare_snp_input.R
POLYFUN_prepare_snp_input.Rd

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(), 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()

Examples

if (FALSE) { # \dontrun{
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)
} # }