In vafisher/AnnoRE: Random Effects Estimation for GWAS Fine Mapping with Functional Annotations

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(AnnoRE)

locus_summary <- annotateREvariance(gwas_locus = locus_gwas_stats, 
                                    annotation = locus_annotation, 
                                    h2partition = ldsc_h2partition)

fine_mapping <- REestimate(loc_summary_df = locus_summary, 
                           trait_h2 = 0.13, 
                           loc_ld_matrix = NULL, 
                           loc_ld_file = system.file("extdata", "locus.1000G.loc.hap.ld", package = "AnnoRE"))
                             #"../inst/extdata/rs3736485.1000G.loc.hap.ld")
head(fine_mapping)

vafisher/AnnoRE documentation built on Dec. 23, 2021, 2:07 p.m.