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Extract instruments locally for MR Analysis

extract_instruments_local.Rd

Filters SNPs by p-value threshold and performs LD clumping with flexible column mapping.

Usage

extract_instruments_local(
  dat,
  p = 5e-08,
  pop = NULL,
  phenotype_col = "Phenotype",
  snp_col = "SNP",
  chr_col = "CHR",
  pos_col = "POS",
  effect_allele_col = "A1",
  other_allele_col = "A2",
  beta_col = "BETA",
  se_col = "SE",
  pval_col = "P",
  eaf_col = "EAF",
  N = "Neff",
  bfile = NULL,
  plink_bin = NULL
)

Arguments

dat

Dataframe containing GWAS summary statistics; change it to dataframe if it is data.table.

p

P-value cutoff (default = 5e-8)

pop

Super-population code for LD reference (default = NULL, as we recommend using loca bfile)

phenotype_col

Column name for phenotype (default = "Phenotype")

snp_col

Column name for SNP IDs (default = "SNP")

chr_col

Column name for chromosome (default = "CHR")

pos_col

Column name for position (default = "POS")

effect_allele_col

Column name for effect allele (default = "A1")

other_allele_col

Column name for non-effect allele (default = "A2")

beta_col

Column name for effect size (default = "BETA")

se_col

Column name for standard error (default = "SE")

pval_col

Column name for p-values (default = "P")

eaf_col

Column name for effect allele frequency (default = "EAF")

N

Column name for sample size (default = "Neff", set NULL to exclude)

bfile

Path to PLINK binary reference panel (default = NULL)

Path to PLINK executable (default = NULL)

Value

Formatted exposure data ready for MR analysis

Examples

if (FALSE) { # \dontrun{
# Custom column names example
extract_instruments_local(
  dat = gwas_data,
  phenotype_col = "Trait",
  snp_col = "rsID",
  chr_col = "Chromosome",
  pos_col = "Position"
)
} # }