Linkage Disequilibrium Shrinkage Estimation for Polyploids

Documentation for package ‘ldsep’ version 2.1.5

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.