Joint effect on phenotype of eQTLs/functional SNPs associated with a gene

Joint effect on phenotype of eQTLs/functional SNPs associated with a gene

Usage

jepeg(
  study_pop,
  input_file,
  annotation_file,
  reference_index_file,
  reference_data_file,
  reference_pop_desc_file,
  af1_cutoff = NULL
)

Arguments

study_pop

study population group

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