getLDscores: Extract Linkage Disequilibrium (LD) Scores

In psoerensen/qgg: Statistical Tools for Quantitative Genetic Analyses

Extract Linkage Disequilibrium (LD) Scores

Description

This function retrieves LD scores from a structured list ('Glist') that includes LD scores, chromosome information, and SNP identifiers. You can extract all LD scores or filter them by a specific chromosome and/or SNP identifiers (rsids).

Usage

getLDscores(Glist = NULL, chr = NULL, rsids = NULL)

Arguments

Glist	A list structure containing genotypic data, including rsids for LD calculation ('rsidsLD'), LD file locations ('ldfiles'), and 'msize' which indicates the size for surrounding region to consider for LD.
chr	A specific chromosome from which LD sets need to be extracted.
rsids	A vector of rsids that need to be included in the sparse LD matrix. Default is NULL, implying all rsids in the chromosome will be used.

Value

A vector containing LD scores.

psoerensen/qgg documentation built on March 29, 2025, 6:36 p.m.