All functions |
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Get the standardized composite D'. |
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Format an element of |
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Obtain the distribution of genotypes given haplotype frequencies under HWE |
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Normalize genotype likelihoods to posterior probabilities. |
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Genotype log-likelihoods from |
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Posterior probabilities from |
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Tests if an argument is a |
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Pairwise LD estimation in polyploids. |
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Estimates of composite pairwise LD based either on genotype estimates or genotype likelihoods. |
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Estimate haplotypic pair-wise LD using either genotypes or genotype likelihoods. |
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Fast bias-correction for LD Estimation |
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Linkage Disequilibrium Shrinkage Estimation for Polyploids |
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Obtain shrinkage estimates of correlation from output of
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Estimate all pair-wise LD's in a collection of SNPs using genotypes or genotype likelihoods. |
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Returns distribution of proportional bivariate normal. |
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Calculate prior variances from a matrix of prior genotype probabilities. |
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Sliding window correlation |
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Sliding window LD estimation |
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Updog fits on the data from Uitdewilligen et. al. (2013) |
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Shrinks Fisher-z transformed correlation estimates and returns resulting correlation estimates. |