Direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts

Direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts

Usage

distmix(
  chr,
  start_bp,
  end_bp,
  wing_size,
  pop_wgt_df,
  input_file,
  reference_index_file,
  reference_data_file,
  reference_pop_desc_file,
  af1_cutoff = NULL
)

Arguments

chr

chromosome number

start_bp

start base pair position of prediction window

end_bp

end base pair position of prediction window

wing_size

the size of the area flanking the left and right of the prediction window

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, af1, 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

Value

R data frame containing rsid, chr, bp, a1, a2, af1mix, z, pval, info, type