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Perform LD clumping on a dataframe based on p-value threshold

finemap_pval_LD.Rd

This function performs linkage disequilibrium (LD) clumping on a given dataframe of genetic association results. The function filters the dataframe based on the provided p-value threshold and then applies the LD clumping for different values of r2. If clumping fails, the function returns a dataframe with NA values in the SNP and test columns.

Usage

finemap_pval_LD(df, bfile, pval_threshold = 5e-08, clump_r2 = 0.001)

Arguments

df

A data frame containing genetic association results with at least the following columns: pval (p-value) and rsid (SNP identifier).

bfile

A character string specifying the prefix for the PLINK binary files (e.g., .bed, .bim, .fam).

pval_threshold

A numeric value specifying the p-value threshold for filtering SNPs. Default is 5E-8.

clump_r2

A numeric vector specifying the r2 threshold(s) for LD clumping. Default is 0.001. The function will perform clumping for each r2 value.

Value

A tibble with columns SNP, test, and LD, where:

  • SNP: the SNPs selected after clumping.

  • test: a character string indicating the test, always "p_ld".

  • LD: the r2 threshold used for clumping.

Examples

# Example usage
if (FALSE) { # \dontrun{
result <- finemap_pval_LD(
  df = my_data,
  bfile = "path_to_bfile",
  pval_threshold = 5E-8,
  clump_r2 = c(0.01, 0.1)
)
} # }