Files in bcm-uga/pcadapt

Fast Principal Component Analysis for Outlier Detection

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/RcppExports.R R/bed2matrix.R R/iram.R R/pcadapt.R R/pcadaptRead.R R/pcadaptUtils.R R/plotUtils.R R/vcfConverter.R R/writebed.R README.md

docs/404.html

docs/articles/index.html

docs/articles/pcadapt.html

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docs/articles/style.css

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

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docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/bed2matrix.html

docs/reference/get.pc.html

docs/reference/get.pop.names.html

docs/reference/get.score.color.html

docs/reference/get_statistics.html

docs/reference/hist_plot.html

docs/reference/index.html

docs/reference/manhattan_plot.html

docs/reference/pcadapt.html

docs/reference/ped2pcadapt.html

docs/reference/plot.pcadapt.html

docs/reference/print_convert.html

docs/reference/qq_plot.html

docs/reference/read.pcadapt.html

docs/reference/run.pcadapt.html

docs/reference/score_plot.html

docs/reference/scree_plot.html

docs/reference/vcf2pcadapt.html

docs/reference/vcf_convert.html

docs/reference/writeBed.html

docs/sitemap.xml

inst/CITATION

inst/WORDLIST

inst/extdata/SSMPG2017.rds

inst/extdata/geno3pops.bed

inst/extdata/geno3pops.bim

inst/extdata/geno3pops.fam

inst/extdata/geno3pops.lfmm

inst/extdata/geno3pops.lfmm.bed

inst/extdata/geno3pops.pcadapt

inst/extdata/geno3pops.pcadapt.bed

inst/extdata/missing.bed

inst/extdata/missing.bim

inst/extdata/missing.fam

inst/extdata/missing.lfmm

inst/extdata/missing.pcadapt

inst/extdata/pool3pops

inst/include/pcadapt/bed-acc.h

inst/include/pcadapt/mat-acc.h

inst/shiny-examples/app-pcadapt/global.R

inst/shiny-examples/app-pcadapt/rsconnect/shinyapps.io/keurcien/app-pcadapt.dcf

inst/shiny-examples/app-pcadapt/server.R inst/shiny-examples/app-pcadapt/server/tab-histogram.R inst/shiny-examples/app-pcadapt/server/tab-manhattan.R inst/shiny-examples/app-pcadapt/server/tab-outlier.R inst/shiny-examples/app-pcadapt/server/tab-pca.R inst/shiny-examples/app-pcadapt/server/tab-rcommand.R inst/shiny-examples/app-pcadapt/server/tab-screeplot.R inst/shiny-examples/app-pcadapt/ui.R inst/shiny-examples/app-pcadapt/ui/helpers.R inst/shiny-examples/app-pcadapt/ui/tab-histogram.R inst/shiny-examples/app-pcadapt/ui/tab-introgression.R inst/shiny-examples/app-pcadapt/ui/tab-local-adaptation.R inst/shiny-examples/app-pcadapt/ui/tab-manhattan.R inst/shiny-examples/app-pcadapt/ui/tab-outlier.R inst/shiny-examples/app-pcadapt/ui/tab-pca.R inst/shiny-examples/app-pcadapt/ui/tab-rcommand.R inst/shiny-examples/app-pcadapt/ui/tab-screeplot.R

inst/shiny-examples/app-pcadapt/www/busy.js

inst/shiny-examples/app-pcadapt/www/style.css

inst/testdata/full.rds

inst/testdata/novar.bed

inst/testdata/novar.bim

inst/testdata/novar.fam

inst/testdata/pcadapt_v3.rds

inst/testdata/to-compare.rds

man/.gitignore

man/bed2matrix.Rd man/get.pc.Rd man/get.pop.names.Rd man/get.score.color.Rd man/get_statistics.Rd man/hist_plot.Rd man/manhattan_plot.Rd man/pcadapt.Rd man/ped2pcadapt.Rd man/plot.pcadapt.Rd man/print_convert.Rd man/qq_plot.Rd man/read.pcadapt.Rd man/run.pcadapt.Rd man/score_plot.Rd man/scree_plot.Rd man/vcf2pcadapt.Rd man/vcf_convert.Rd man/writeBed.Rd

new-paper/.gitignore

new-paper/code/1-compare-timings-versions.R new-paper/code/2-generate-missing-matrices.R new-paper/code/3-run-missing.R new-paper/code/4-missingness-results.R

new-paper/compare-with-missing.png

new-paper/compare-with-old.png

new-paper/install-tex-pkgs.R

new-paper/natbib.bst

new-paper/natbib.sty

new-paper/new-paper.Rproj

new-paper/paper-pcadapt-v4-supp.tex

new-paper/paper-pcadapt-v4.tex

new-paper/refs.bib

new-paper/timings.pdf

pcadapt.Rproj

src/.gitignore

src/Makevars

src/RcppExports.cpp

src/af.cpp

src/bed-acc-xptr.cpp

src/bed2matrix.cpp

src/clumping.cpp

src/linear-regression.cpp

src/nb-na.cpp

src/pedUtils.cpp

src/prodMat.cpp

src/total-var.cpp

src/vcfUtils.cpp

src/writebed.cpp

tests/spelling.R tests/testthat.R tests/testthat/test_convert.R tests/testthat/test_missing.R tests/testthat/test_read.R tests/testthat/test_var_expl.R tests/testthat/test_version.R

tmp-save/bed-col-acc.cpp

tmp-save/bedadapt.h

tmp-save/get-hapmap-data.R

tmp-save/linear-regression-bad.cpp

tmp-save/linear-regression-noapprox.cpp

tmp-save/novar-data.R

tmp-save/ogk.cpp

tmp-save/pcadapt.R

tmp-save/test.cpp

tmp-tests/COMPARE-BEFORE.R tmp-tests/Check_package_privefl.R tmp-tests/WG_pcadapt_10x.R tmp-tests/fp.R

tmp-tests/getCode.cpp

tmp-tests/mv_nunif_0.2.pcadapt

tmp-tests/test-af.R

tmp-tests/test-div4.cpp

tmp-tests/test-eigen-crossprod.cpp

tmp-tests/test-iram.R

tmp-tests/test-isna_int.cpp

tmp-tests/test-na.cpp

tmp-tests/test-pcadapt.R tmp-tests/test-pool.R tmp-tests/test-popres.R tmp-tests/test-prod.R tmp-tests/test-vcf-ped.R tmp-tests/test-writeBed.R tmp-tests/test_missing_data.R tmp-tests/test_pooledseq_K=1.R tmp-tests/test_pooledseq_Keurcien.R

tmp-tests/try-bug.cpp

tmp-tests/zscores-noapprox.png

vignettes/pcadapt.Rmd

vignettes/style.css

bcm-uga/pcadapt documentation built on April 17, 2024, 8:30 a.m.