FINEMAP_construct_data: Prepare input files for 'FINEMAP'

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

Prepare input files for FINEMAP

Description

Creates and saves 1) the summary stats file, and 2) the LD matrix. "Columns beta and se are required for fine-mapping. Column maf is needed to output posterior effect size estimates on the allelic scale. All other columns are not required for computations and can be specified arbitrarily."

Usage

FINEMAP_construct_data(dat, locus_dir, LD_matrix, nThread = 1, verbose = TRUE)

Source

http://www.christianbenner.com

locus_dir <- echodata::locus_dir; dat <- echodata::BST1; LD_matrix <- echodata::BST1_LD_matrix dir.create(file.path(locus_dir,"FINEMAP"), showWarnings = FALSE, recursive = TRUE) out <- echoLD::subset_common_snps(LD_matrix=LD_matrix, dat=dat) LD_matrix <- out$LD dat <- out$DT dat_paths <- echofinemap:::FINEMAP_construct_data(dat=dat, locus_dir=locus_dir, LD_matrix=LD_matrix)

See Also

Other FINEMAP: FINEMAP_construct_master(), FINEMAP_find_executable(), FINEMAP_process_results(), FINEMAP()

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