Build LD matrix from a PLINK dosage export

Reads a PLINK2 --export A .raw file. Extracts the "counted" allele from the column name suffix (e.g., rs123_A -> A) to provide exact allele orientation without relying on EAF.

Usage

ld_matrix(raw_path)

Arguments

raw_path

Path to the .raw file.

Value

List with G (dosages), R (correlation LD), ids, freq, and counted allele.