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 with the population abbreviation in the first column and its mixing proportion in the second, read positionally. Proportions must be non-negative; they are rescaled to sum to 1, which the mixture covariance assumes. See data(PGC2_SCZ_ANC_Prop) for the expected shape. Note that afmix() returns three columns, so its first column must be dropped first.
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