Estimate haplotypic 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 ldfast(), ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2021a) <doi:10.1111/1755-0998.13349> and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.
Version: 2.1.5 Depends: R (≥ 2.10) Imports: Rcpp, foreach, doParallel, ashr, corrplot, lpSolve, abind, modeest, matrixStats LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, covr, knitr, rmarkdown, updog (≥ 2.0.2), VariantAnnotation Published: 2022-10-18 DOI: 10.32614/CRAN.package.ldsep 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 Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=ldsep to link to this page.
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