Linkage Disequilibrium Shrinkage Estimation for Polyploids


[Up] [Top]

Documentation for package ‘ldsep’ version 1.0.0

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
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_gam Estimate gametic pair-wise LD using either genotypes or genotype likelihoods.
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()'
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.