ldsep

ldsep estimates linkage disequilibrium (LD) in polyploids from genotypes or genotype likelihoods, providing haplotypic and composite pairwise LD measures for analyses that include the LD coefficient D, the standardized coefficient D', and the Pearson correlation r.

Key Features:

• LD Estimation: Estimates haplotypic and composite pairwise LD measures, including D, D', and Pearson correlation r, directly from genotypes or genotype likelihoods.
• Handling Genotype Uncertainty: Utilizes genotype likelihoods to account for genotype uncertainty inherent to polyploid genotyping.
• Standard Error Calculation: Computes standard errors for all LD estimates to quantify estimation uncertainty.
• Shrinkage Estimation: Performs shrinkage estimation using LD measures and their standard errors to refine estimates.
• Provided Functions: Includes ldest() for LD coefficient estimation, mldest() for maximum likelihood estimation from genotype likelihoods, sldest() for shrinkage estimates, plot.lddf() to visualize LD decay, and format_lddf() to format LD decay outputs.

Scientific Applications:

• Polyploid linkage analysis: Enables estimation of LD for mapping traits in polyploid genomes.
• Candidate gene mapping: Supports identification of candidate genes by characterizing local LD patterns.
• Evolutionary genetics: Facilitates studies of population-level LD and evolutionary processes in polyploid species.

Methodology:

Characterizes haplotypic and composite LD measures; derives estimation procedures that operate directly on genotype likelihoods, including maximum likelihood estimation via mldest(); computes standard errors for LD estimates and applies shrinkage estimation using those standard errors; methods validated on real and simulated datasets.