JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts

Usage

jepegmix(
  pop_wgt_df,
  input_file,
  annotation_file,
  reference_index_file,
  reference_data_file,
  reference_pop_desc_file,
  af1_cutoff = NULL
)

Arguments

pop_wgt_df: R data frame containing population IDs and weights
input_file: file name of GWAS summary statistics data containing rsid, chr, bp, a1, a2 and z
reference_index_file: file name of reference panel index data
reference_data_file: file name of reference panel data
reference_pop_desc_file: file name of reference panel population description data
af1_cutoff: cutoff of reference allele, a1, frequency
annotation: file name of the SNP annotation data set

Value

R dataframe containing geneid, chisq, df, jepeg_pval, num_snp, top_categ, top_categ_pval, top_snp, and top_snp_pval