Code

Ploidy#36

Code

Merged

dramanica merged 36 commits intomainEvolEcolGroup/tidypopgen:mainfrom ploidyEvolEcolGroup/tidypopgen:ploidyCopy head branch name to clipboardMay 13, 2024

+1,187-117

Commits

Commits on Apr 20, 2024

• store ploidy info (all fixed to diploid)

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• example dataset

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Commits on Apr 21, 2024

• correctly track ploidy from matrix

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• better handling of ploidy

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• speed up alt_freq

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• fix subsetting

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• tidy docs

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Commits on Apr 22, 2024

• compute frequency in polyploids

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• add loci missingness for polyploids

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• make indiv_missingness faster and work with polyploids

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Commits on Apr 23, 2024

• Merge branch 'ploidy' of github.com:EvolEcolGroup/tidypopgen into ploidy

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Commits on May 3, 2024

• count_vcf_variants

  

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• Resolve dapc conflict

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• Resolve gen_tibble conflict

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• Implement loci_maf()

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• test gen_tibble error

  

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• Add count_vcf_individuals

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• Format gt_vcf_to_bed.R

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• First attempy at vcf to fbm function. Note, not added to tests, or into namespace yet.

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• Merge branch 'main' into ploidy

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• resolve merge issues

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• small clean up

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Commits on May 10, 2024

• Merge branch 'main' into ploidy

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• clean up to have a ploidy example

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• keep some functions as internal

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• adapt vcf for ploidy

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• adapt vcf_to_fbm to deal with ploidy

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• remove examples for internal functions

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Commits on May 11, 2024

• initial implementation of vcf reading for ploidy

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• vcf fix

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Commits on May 13, 2024

• add test data vcfs

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• Merge pull request #35 from EvolEcolGroup/add_vcfs

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• test vcf input

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• improve warning message

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• clean up test files

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• improve vcf tests

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