Computes the D', Wn, and conditional asymmetric linkage disequilibrium (ALD) measures for pairs of genetic loci. Performs these linkage disequilibrium (LD) calculations on phased genotype data recorded using Genotype List (GL) String or columnar formats. Alternatively, generates expectation-maximization (EM) estimated haplotypes from phased data, or performs LD calculations on EM estimated haplotypes. Performs sign tests comparing LD values for phased and unphased datasets, and generates heat-maps for each LD measure. Described by Osoegawa et al. (2019a) <doi:10.1016/j.humimm.2019.01.010>, and Osoegawa et. al. (2019b) <doi:10.1016/j.humimm.2019.05.018>.
| Version: | 1.0.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | haplo.stats, gap, stats, utils, ggplot2, reshape2, BIGDAWG, graphics |
| Suggests: | knitr, rmarkdown |
| Published: | 2020-04-15 |
| Author: | Steven Mack [aut, cre] |
| Maintainer: | Steven Mack <steven.mack at ucsf.edu> |
| License: | GPL (≥ 3) |
| NeedsCompilation: | no |
| Materials: | README NEWS |
| CRAN checks: | pould results |
| Reference manual: | pould.pdf |
| Vignettes: |
Using pould |
| Package source: | pould_1.0.0.tar.gz |
| Windows binaries: | r-devel: pould_1.0.0.zip, r-release: pould_1.0.0.zip, r-oldrel: pould_1.0.0.zip |
| macOS binaries: | r-release: pould_1.0.0.tgz, r-oldrel: pould_1.0.0.tgz |
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