# Linkage Disequilibrium Shrinkage Estimation for Polyploids

## Documentation for package ‘ldsep’ version 2.1.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ldsep-package | Linkage Disequilibrium Shrinkage Estimation for Polyploids
Dprime | Get the standardized composite D'.
format_lddf | Format an element of 'mldest()' or 'sldest()' into an upper-triangular matrix.
get_prob_array | Obtain the distribution of genotypes given haplotype frequencies under HWE
glike | Genotype log-likelihoods from 'uit'
gl_to_gp | Normalize genotype likelihoods to posterior probabilities.
gp | Posterior probabilities from 'uit'
is.lddf | Tests if an argument is a 'lddf' object.
ldest | Pairwise LD estimation in polyploids.
ldest_comp | Estimates of composite pairwise LD based either on genotype estimates or genotype likelihoods.
ldest_hap | Estimate haplotypic pair-wise LD using either genotypes or genotype likelihoods.
ldfast | Fast bias-correction for LD Estimation
ldsep | Linkage Disequilibrium Shrinkage Estimation for Polyploids
ldshrink | Obtain shrinkage estimates of correlation from output of 'mldest()' or 'sldest()'.
mldest | Estimate all pair-wise LD's in a collection of SNPs using genotypes or genotype likelihoods.
pbnorm_dist | Returns distribution of proportional bivariate normal.
plot.lddf | Plot the output of 'mldest()' or 'sldest()' using 'corrplot()'
pvcalc | Calculate prior variances from a matrix of prior genotype probabilities.
slcor | Sliding window correlation
sldest | Sliding window LD estimation
uit | Updog fits on the data from Uitdewilligen et. al. (2013)
zshrink | Shrinks Fisher-z transformed correlation estimates and returns resulting correlation estimates.