Compute LD for measured SNPs from mixed ethnicity cohorts
Usage
computeLD(
chr,
start_bp,
end_bp,
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
- 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, 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