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Betabinomial alpha estimation
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@doddsk
doddsk committed Dec 2, 2024
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@doddsk doddsk commented on 5500113 Dec 2, 2024

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Changes in v1.3.0 (3/12/2024)

  • added nix packaging
  • better handling of nind=1 and nsnps=1 cases
  • GBSsummary - iterate sample and SNP checks until no more SNPs removed.
  • posCreport - when there is a failed identity check involving at least 3 genotypes, the genotypes (seqIDs) are grouped into consistent sets.
  • redosamples - function to create (a new version of) the samples object
  • alleles2g - function for creating genon and/or depth from alleles
  • Inbsampled - function for estimating inbreeding from merged allele samples
  • bbinit - function for creating/updating a data frame of beta-binomial alpha values
  • bbestimate - function for estimating beta-binomial alpha values
  • bbeffdepth - function to convert depths to effective depths based on a set of beta-binomial alpha values for each sample
  • calcGdiag, mergeSamples - retrieve undefined objects from the environment where the function was called from (previously from the global environment, i.e. where these functions were defined).
  • PedAssign - doublemm setting for (count cases where both sire and dam are mismatches as 2 in trio mismatch counts)

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