Man pages for ldsep
Linkage Disequilibrium Shrinkage Estimation for Polyploids
| Dprime | Get the standardized composite D'. |
| format_lddf | Format an element of 'mldest()' or 'sldest()' into an... |
| get_prob_array | Obtain the distribution of genotypes given haplotype... |
| 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... |
| ldest_hap | Estimate haplotypic pair-wise LD using either genotypes or... |
| ldfast | Fast bias-correction for LD Estimation |
| ldsep-package | Linkage Disequilibrium Shrinkage Estimation for Polyploids |
| ldshrink | Obtain shrinkage estimates of correlation from output of... |
| mldest | Estimate all pair-wise LD's in a collection of SNPs using... |
| pbnorm_dist | Returns distribution of proportional bivariate normal. |
| plot.lddf | Plot the output of 'mldest()' or 'sldest()' using... |
| pvcalc | Calculate prior variances from a matrix of prior genotype... |
| 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... |
