polyRAD 2.0.1

• Bug fix in TestOverdispersion when the optimal value is the minimum tested.
• VCF2RADdata now can make use of .csi indices on VCFs that are already bgzipped.
• Bug fix in Export_MAPpoly relating to how ploidy is coded.
• Bug fix in AddAlleleFreqByTaxa if only one PC is used.
• Update readStacks for new file formats.
• Update Bioconductor links to pass CRAN checks

polyRAD 2.0

• Multiploid populations are now supported. This includes natural populations with variable ploidy, as well as better support for mapping populations such as triploid populations derived from diploid x tetraploid crosses. Internally, slots containing genotype prior probabilities, likelihoods, and posterior probabilities are now formatted as two-dimensional lists, with possible inheritance modes across loci in the first dimension and varying ploidy across taxa in the second dimension, whereas previously these were one-dimensional lists reflecting inheritance modes across loci only. The priorProbPloidies slot has been removed as it is no longer needed.

• The ExamineGenotype function has been added.

• The AddPriorTimesLikelihood function has been removed.

• A warning is now returned if the user attempts to simulate self-fertilization in odd-ploidy individuals (i.e. using the selfing.rate argument in IterateHWE and related functions). The selfing rate is set to zero in these individuals to prevent an error.

• IteratePopStruct and IteratePopStructLD now have an argument called maxR2changeratio to allow more fine-tuning of the number of principal components used.

• The readDArTag function has been updated to support a newer format from Excellence in Breeding, as well as their original format.

• MergeIdenticalHaplotypes now takes IUPAC ambiguity codes into account. It is now used internally by VCF2RADdata, readStacks, readTASSELGBSv2, and readProcessIsoloci. Some additional loci will now be filtered out by these functions.

• GetProbableGenotypes with multiallelic = "correct", and by extension RADdata2VCF, now run much faster by searching a much narrower range of possible multiallelic genotypes.

• Optimizations to improve speed of data import.

• Bug fix in MergeRareHaplotypes when some alleles have zero reads.

polyRAD 1.6

• TestOverdispersion now prints a helpful suggestion for which overdispersion parameter to use, as well as returning that value in its output. The use of qqman has been eliminated from the vignettes.

• ExpectedHindHe, ExpectedHindHeMapping, and SimAlleleDepth now have a contamRate parameter to simulate sample cross contamination when sampling allelic read depth, and an errorRate parameter to simulate sequencing error.

• A bug has been fixed in Export_GWASpoly so that special characters in sample names are not converted to periods.

polyRAD 1.5

• SimGenotypesMapping, ExpectedHindHeMapping, Export_polymapR_probs, reverseComplement, and readDArTag functions added.

• Bug fixed in GetProbableGenotypes when there are multiple possiblePloidies and multiallelic is set to "na" or "correct".

• Bug fixed in process_sam_multi.py for cases where sample names contain spaces.

• Bug fixed in HindHeMapping when loci are discarded due to difficulty estimating parental genotypes.

• Vignettes have been updated with a figure to assist in estimating inbreeding.

polyRAD 1.4

• Export_GWASpoly can now export posterior mean genotypes.

• Export_adegenet_genind function added.

polyRAD 1.3

• Added the ExpectedHindHe, SimGenotypes, and SimAlleleDepth functions. The first in particular is intended to help the user to select a Hind/He threshold for filtering markers.

• Added the Export_Structure function.

• In the variant calling pipeline, process_isoloci.py has been modified so that the user can set an expected and maximum Hind/He. The previous functionality, where these thresholds were calculated automatically from inbreeding, remains available.

• Fixed a bug in VCF2RADdata that would occur if expectedAlleles or expectedLoci were set too low. VCF2RADdata now also sets the "Variable_sites_only" attribute to be FALSE if phaseSNPs = FALSE.

• Fixed a bug in SubsetByLocus, MergeRareHaplotypes, and MergeIdenticalHaplotypes that would delete the "Variable_sites_only" attribute, preventing VCF export.

polyRAD 1.2

• The functions HindHe and HindHeMapping have been added, to assist with filtering loci that are behaving in a non-Mendelian fashion, as well as individuals that do not behave like the expected ploidy. The function InbreedingFromHIndHe has been added to facilitate estimating the inbreeding statistic F from the results of HindHe.

• The Python scripts process_sam_multi.py and process_isoloci.py have been added, to serve as a pipeline for variant calling in highly duplicated genomes. These are described in a new vignette, “Variant and Genotype Calling in Highly Duplicated Genomes” (isolocus_sorting.Rmd). The functions readProcessSamMulti and readProcessIsoloci have been added for import of data from the Python scripts into polyRAD.

• The function RADdata2VCF has been added for export to VCF.

• A Python script has been added to help identify full tag sequences for alleles imported from TASSEL-GBSv2 using VCF2RADdata.

• The GetProbableGenotypes function has been updated to optionally recognize genotypes where copy number does not sum to the ploidy across all alleles for a locus. It can now either set these genotypes to NA or correct them to sum to the ploidy. Some internal Rcpp functions were added for this purpose.

• A bug has been fixed in SubsetByPloidy.

• MergeTaxaDepth now generates a more useful error if taxa are specified that do not exist in the object.

• If duplicate locus names are passed to SubsetByLocus, it now generates a warning and deals with the duplicated loci more appropriately.

• The AddDepthSamplingPermutations function has been added. Permutations for estimating genotype likelihoods are no longer calculated at the time of data import, but instead are calculated the first time that genotype likelihoods are calculated. This is to avoid unnessasary calculation and recalculation when alleles and taxa are filtered or merged before running genotype calling. From the user perspective, there isn’t any change except faster import.

• The EstimateParentalGenotypes function has been added, using code that was previously in the AddGenotypePriorProb_Mapping2Parents. This does not impact anything from the user’s perspective, but makes the code slightly less unwieldy and allows parental genotype estimations to be used for other purposes.

• The MergeIdenticalHaplotypes function has been added.

• Internal functions for simulating gametes and calculating their frequencies have been corrected so that they still work when only one allele is being simulated.

polyRAD 1.1

• A plot method has been added for RADdata objects.

• The MergeTaxaDepth, RemoveUngenotypedLoci, and SubsetByPloidy utility functions have been added.

• The Export_MAPpoly and Export_GWASpoly functions have been added.

• Bug fixes have been made in TestOverdispersion, VCF2RADdata, SubsetByLocus, and SubsetByTaxon.

• Some code in AddAlleleFreqByTaxa has been translated to Rcpp to speed computation time for IteratePopStruct and IteratePopStructLD.

polyRAD 1.0

• Genotype likelihoods are now estimated under a beta-binomial distribution rather than the binomial distribution. This change was made so that real sequencing data would be accurately modeled; even in diploid heterozygotes, read depth of two alleles is often very different from a 1:1 ratio, due to many underlying issues with sequencing data that would be difficult to model. Under the beta-binomial with respect to the binomial, there is an increased probability of read depth ratios that differ from the true allele copy ratio. In a practical sense, this means reduced certainty in the estimation of allele copy number from read depth alone, and an increased importance of genotype prior probabilities. The exact shape of the beta-binomial distribution is determined by an overdispersion parameter, which the user can optimize using the TestOverdispersion function.

• When using linkage disequilibrium to update genotype priors, the square of Pearson’s correlation coefficient is now used for weighting markers, where Pearson’s correlation coefficient was used previously without being squared. This applies to both mapping populations and diversity panels, and results in improved genotyping accuracy.

• The functions Export_polymapR, readTASSELGBSv2, RemoveHighDepthLoci, AddGenotypePriorProb_Even, and TestOverdispersion have been added.

• This version of polyRAD is incompatible with RADdata objects generated by previous versions of polyRAD due to a change in format of the depthSamplingPermutations slot. This slot was changed to simplify the estimation of genotype likelihood.