[aut, cre]Estimate gametic or composite pairwise linkage disequilibrium (LD) in polyploids, using either genotypes or genotype likelihoods. Support is provided to estimate the popular measures of LD: the LD coefficient D, the standardized LD coefficient D', and the Pearson correlation coefficient r. All estimates are returned with corresponding standard errors. These estimates and standard errors can then be used for shrinkage estimation. The main functions are ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink().
| Version: | 1.0.0 |
| Depends: | R (≥ 2.10) |
| Imports: | Rcpp, foreach, doParallel, ashr, corrplot, lpSolve |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | testthat, covr, knitr, rmarkdown, updog (≥ 2.0.2) |
| Published: | 2020-08-02 |
| Author: | David Gerard
[aut, cre] |
| Maintainer: | David Gerard <gerard.1787 at gmail.com> |
| BugReports: | https://github.com/dcgerard/ldsep/issues |
| License: | GPL-3 |
| NeedsCompilation: | yes |
| Citation: | ldsep citation info |
| Materials: | README NEWS |
| CRAN checks: | ldsep results |
| Reference manual: | ldsep.pdf |
| Vignettes: |
Example Pipeline for Estimating LD |
| Package source: | ldsep_1.0.0.tar.gz |
| Windows binaries: | r-devel: ldsep_1.0.0.zip, r-release: ldsep_1.0.0.zip, r-oldrel: ldsep_1.0.0.zip |
| macOS binaries: | r-release: ldsep_1.0.0.tgz, r-oldrel: ldsep_1.0.0.tgz |
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