Files in TomerAntman/VCFtoGWAS
Get GWAS out of VCF file
.Rbuildignore
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.gitignore
.idea/VCFtoGWAS.iml
.idea/modules.xml
DESCRIPTION
NAMESPACE
NEWS.md
R/Build_offspring_GWAS_matrix.R
R/Create_complete_snp_data.R
R/Creating_joint_density_plot.R
R/Expand_files.R
R/Filter_genotypes.R
R/GWAS_conclusions.R
R/Get_GWAS_matrix.R
R/Save_GWAS.R
R/Save_as_RDS.R
R/Upload_vcf_to_R.R
R/Used_Packages.R
R/allele_presence_plot.R
R/create_SacCer_sgd_cds.R
R/create_directory.R
R/create_gData.R
R/name_by_time.R
R/plot_manhattan.R
R/polygenic_effect_score.R
R/show_suggested_data_structure.R
README.md
VCFtoGWAS.Rproj
_pkgdown.yml
data/SacCer_sgd_cds.rda
docs/404.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
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docs/apple-touch-icon.png
docs/articles/.idea/articles.iml
docs/articles/.idea/modules.xml
docs/articles/1) General.html
docs/articles/2) Chapter 1.html
docs/articles/3) Chapter 2.html
docs/articles/ManhatUfit_60.svg
docs/articles/ManhattanResult.png
docs/articles/ManhattanStatgen.png
docs/articles/QQResults.png
docs/articles/QQresultsYfit.svg
docs/articles/Ubinfit_alleleVSfit.png
docs/articles/Ubinfit_alleleVSfit.svg
docs/articles/Ubinfit_polscore.png
docs/articles/Ufit_alleleVSfit.png
docs/articles/Ufit_alleleVSfit.svg
docs/articles/Ufit_polscore.png
docs/articles/VCF_demo1.png
docs/articles/index.html
docs/articles/package_intro.html
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docs/authors.html
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docs/deps/bootstrap-5.1.0/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
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docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Build_offspring_GWAS_matrix.html
docs/reference/Create_complete_snp_data.html
docs/reference/Expand_files.html
docs/reference/Filter_genotypes.html
docs/reference/Rplot001.png
docs/reference/Upload_vcf_to_R.html
docs/reference/allele_presence_plot.html
docs/reference/create_SacCer_sgd_cds.html
docs/reference/create_directory.html
docs/reference/figures/ManhattanResult.png
docs/reference/figures/ManhattanStatgen.png
docs/reference/figures/QQResults.png
docs/reference/figures/Ubinfit_alleleVSfit.png
docs/reference/figures/Ubinfit_polscore.png
docs/reference/figures/Ufit_alleleVSfit.png
docs/reference/figures/Ufit_poleffect.png
docs/reference/figures/Ufit_polscore.png
docs/reference/figures/VCF_demo1.png
docs/reference/figures/logo.png
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docs/reference/figures/step2.2Output.png
docs/reference/figures/vcfCartoon.png
docs/reference/index.html
docs/reference/name_by_time.html
docs/reference/show_suggested_data_structure.html
docs/search.json
docs/sitemap.xml
man/Build_offspring_GWAS_matrix.Rd
man/Create_complete_snp_data.Rd
man/Expand_files.Rd
man/Filter_genotypes.Rd
man/Upload_vcf_to_R.Rd
man/allele_presence_plot.Rd
man/create_SacCer_sgd_cds.Rd
man/create_directory.Rd
man/figures/logo.png
man/name_by_time.Rd
man/show_suggested_data_structure.Rd
myalignment.tex
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
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pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
vignettes/.gitignore
vignettes/1) General.Rmd
vignettes/2) Chapter 1.Rmd
vignettes/3) Chapter 2.Rmd
vignettes/ManhatUfit_60.svg
vignettes/ManhattYfit_99.svg
vignettes/ManhattanResult.png
vignettes/ManhattanStatgen.png
vignettes/QQResults.png
vignettes/QQresultsYfit.svg
vignettes/Ubinfit_alleleVSfit.png
vignettes/Ubinfit_alleleVSfit.svg
vignettes/Ubinfit_polscore.png
vignettes/Ufit_alleleVSfit.png
vignettes/Ufit_alleleVSfit.svg
vignettes/Ufit_poleffect.png
vignettes/Ufit_polscore.png
vignettes/VCF_demo1.png
vignettes/step1.1Output.png
vignettes/step1.2Output.png
vignettes/step1.3Output.png
vignettes/step1.4Output.png
vignettes/step2.2Output.png
vignettes/vcfCartoon.png
