Linkage Disequilibrium Shrinkage Estimation for Polyploids
Get the standardized composite D'.
Format an element of mldest() or sldest() into an upper-triangular...
Obtain the distribution of genotypes given haplotype frequencies under...
Normalize genotype likelihoods to posterior probabilities.
Tests if an argument is a lddf object.
Pairwise LD estimation in polyploids.
Estimates of composite pairwise LD based either on genotype estimates ...
Estimate haplotypic pair-wise LD using either genotypes or genotype li...
Fast bias-correction for LD Estimation
Linkage Disequilibrium Shrinkage Estimation for Polyploids
Obtain shrinkage estimates of correlation from output of mldest() or...
Estimate all pair-wise LD's in a collection of SNPs using genotypes or...
Returns distribution of proportional bivariate normal.
Plot the output of mldest() or sldest() using corrplot()
Calculate prior variances from a matrix of prior genotype probabilitie...
Sliding window correlation
Sliding window LD estimation
Shrinks Fisher-z transformed correlation estimates and returns resulti...
Estimate haplotypic or composite pairwise linkage disequilibrium (LD) in polyploids, using either genotypes or genotype likelihoods. Support is provided to estimate the popular measures of LD: the LD coefficient D, the standardized LD coefficient D', and the Pearson correlation coefficient r. All estimates are returned with corresponding standard errors. These estimates and standard errors can then be used for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2021a) <doi:10.1111/1755-0998.13349> and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.