ldsep
Linkage Disequilibrium Shrinkage Estimation for Polyploids
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.
- Version2.1.5
- R versionunknown
- LicenseGPL-3
- Needs compilation?Yes
- ldsep citation info
- Last release10/18/2022
Documentation
Team
David Gerard
Insights
Last 30 days
This package has been downloaded 184 times in the last 30 days. Enough downloads to make a small wave in the niche community. The curiosity is spreading! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 7 times.
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Last 365 days
This package has been downloaded 2,964 times in the last 365 days. Consider this 'mid-tier influencer' status—if it were a TikTok, it would get a nod from nieces and nephews. The day with the most downloads was Jan 30, 2025 with 52 downloads.
The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.
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Dependencies
- Imports9 packages
- Suggests5 packages
- Linking To2 packages