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. |