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

annotation_file

file name of the SNP annotation data: a whitespace-delimited table with a header line and the columns rsid, chr, bp, a1, a2, geneid, categ, wgt. Variants are matched to the study data by (chr, bp, a1, a2) in either allele order, never by rsid, so rsid may be given as .. categ must be one of PROTEIN, TFBS, WTH_HAIR, WTH_TARGET, CIS_EQTL or TRANS_EQTL, reported in the result as PFS, TFB, STR, TAR, CIS and TRN respectively; rows carrying any other value are skipped and counted in a warning. wgt is the variant's weight within its category.

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

Value

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