finds proxy SNPs from an internal reference split the SNP search into 10k blocks

Usage

proxy_search_split(
  data_exposure,
  data_outcome,
  data_outcome_path,
  data_reference,
  data_reference_path,
  tag_r2 = 0.8,
  tag_kb = 5000,
  tag_nsnp = 5000,
  outcome_sep,
  outcome_phenotype,
  outcome_SNP,
  outcome_BETA,
  outcome_SE,
  outcome_P,
  outcome_EA,
  outcome_OA,
  outcome_EAF,
  outcome_N,
  outcome_ID,
  outcome_CHR,
  outcome_POS
)

Arguments

data_exposure: Data frame containing exposure SNP data.
data_outcome: Data frame containing outcome SNP data.
data_outcome_path: Path to the outcome data file.
data_reference: Data frame containing reference SNP data.
data_reference_path: Path to the reference data file.
tag_r2: Threshold for LD (default: 0.8).
tag_kb: Threshold for distance in kb (default: 5000).
tag_nsnp: Threshold for number of SNPs (default: 5000).
outcome_sep: Delimiter used in the outcome data file.
outcome_phenotype: Column name for the outcome phenotype.
outcome_SNP: Column name for the SNP in the outcome data.
outcome_BETA: Column name for the beta value in the outcome data.
outcome_SE: Column name for the standard error in the outcome data.
outcome_P: Column name for the p-value in the outcome data.
outcome_EA: Column name for the effect allele in the outcome data.
outcome_OA: Column name for the other allele in the outcome data.
outcome_EAF: Column name for the effect allele frequency in the outcome data.
outcome_N: Column name for the sample size in the outcome data.
outcome_ID: Column name for the ID in the outcome data.
outcome_CHR: Column name for the chromosome in the outcome data.
outcome_POS: Column name for the position in the outcome data.

Value

Data frame with proxy SNPs added.