Files in bcm-uga/pcadapt
Fast Principal Component Analysis for Outlier Detection

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/RcppExports.R R/bedadapt.R R/imputation.R R/introUtils.R R/manhattan-plot.R R/pcadapt.R R/pcadaptClass.R R/pcadaptStat.R R/pcadaptUtils.R R/plotUtils.R R/poolUtils.R R/qq-plot.R R/rdadapt.R R/sandbox.R R/score-plot.R R/scree-plot.R R/svd.R R/vcfConverter.R README.md
_pkgdown.yml
docs/_config.yml
docs/articles/index.html
docs/articles/pcadapt.R
docs/articles/pcadapt.html
docs/articles/pcadapt_files/figure-html/unnamed-chunk-10-1.png
docs/articles/pcadapt_files/figure-html/unnamed-chunk-11-1.png
docs/articles/pcadapt_files/figure-html/unnamed-chunk-12-1.png
docs/articles/pcadapt_files/figure-html/unnamed-chunk-15-1.png
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docs/articles/pcadapt_files/figure-html/unnamed-chunk-20-1.png
docs/articles/pcadapt_files/figure-html/unnamed-chunk-22-1.png
docs/articles/pcadapt_files/figure-html/unnamed-chunk-7-1.png
docs/articles/pcadapt_files/figure-html/unnamed-chunk-8-1.png
docs/articles/style.css
docs/articles/tuto_fdr.html
docs/articles/tuto_fdr_files/figure-html/unnamed-chunk-5-1.png
docs/articles/tuto_introgression.html
docs/articles/tuto_introgression_files/figure-html/unnamed-chunk-9-1.png
docs/articles/tuto_pca.html
docs/articles/tuto_pca_files/figure-html/unnamed-chunk-2-1.png
docs/articles/tuto_pca_files/figure-html/unnamed-chunk-3-1.png
docs/articles/tuto_pca_files/figure-html/unnamed-chunk-4-1.png
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/reference/BED_rsvd.html
docs/reference/BED_rsvd_missing.html
docs/reference/assign.int.labels.html
docs/reference/bedadapt-class.html
docs/reference/cart2bary_cpp.html
docs/reference/check_row.html
docs/reference/clumping.html
docs/reference/cmpt.stat.html
docs/reference/cmpt_all_stat.html
docs/reference/cmpt_centroids.html
docs/reference/cmpt_cov_cpp.html
docs/reference/cmpt_directional_stat.html
docs/reference/cmpt_global_pca.html
docs/reference/cmpt_loadings.html
docs/reference/cmpt_local_pca.html
docs/reference/cmpt_minor_af.html
docs/reference/cmpt_transformation.html
docs/reference/cmpt_wilcoxon_stat.html
docs/reference/covRob_cpp.html
docs/reference/create.pcadapt.html
docs/reference/display.local.pca.html
docs/reference/draw.pca.html
docs/reference/get.output.name.html
docs/reference/get.pc.html
docs/reference/get.pool.matrix.html
docs/reference/get.pop.names.html
docs/reference/get.score.color.html
docs/reference/get_axis.html
docs/reference/get_nb_ind.html
docs/reference/get_pop_size.html
docs/reference/get_rank.html
docs/reference/get_size_cpp.html
docs/reference/get_window.html
docs/reference/impute.pcadapt.html
docs/reference/impute_geno.html
docs/reference/impute_geno_pop.html
docs/reference/index.html
docs/reference/lfmm2pcadapt.html
docs/reference/loc.anc.plotting.html
docs/reference/lrfunc_cpp.html
docs/reference/manhattan.plotting.html
docs/reference/median_per_pop.html
docs/reference/median_row_i.html
docs/reference/neutral.plotting.html
docs/reference/pca_rotation.html
docs/reference/pcadapt-package.html
docs/reference/pcadapt.html
docs/reference/ped2pcadapt.html
docs/reference/plot.pcadapt.html
docs/reference/print_convert.html
docs/reference/pvalqq.plotting.html
docs/reference/rdadapt.html
docs/reference/read.pcadapt.html
docs/reference/rescale_local_pca.html
docs/reference/residuals_to_stat.html
docs/reference/run.pcadapt.html
docs/reference/sample_geno_file.html
docs/reference/sample_geno_matrix.html
docs/reference/scale_geno.html
docs/reference/scan.intro.html
docs/reference/score.plotting.html
docs/reference/scree.plotting.html
docs/reference/slidingWindows_fast.html
docs/reference/slidingWindows_new.html
docs/reference/svd.pcadapt.html
docs/reference/updt_local_scores.html
docs/reference/vcf2pcadapt.html
docs/reference/vcf_convert.html
inst/extdata/geno3pops.lfmm
inst/extdata/geno3pops.loadings
inst/extdata/geno3pops.maf
inst/extdata/geno3pops.pcadapt
inst/extdata/geno3pops.scores
inst/extdata/geno3pops.sigma
inst/extdata/geno3pops.zscores
inst/extdata/pool3pops
inst/include/pcadapt/bedadapt.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
man/.gitignore
man/BED_rsvd.Rd man/assign.int.labels.Rd man/bedadapt-class.Rd man/cart2bary_cpp.Rd man/clumping.Rd man/cmpt.stat.Rd man/cmpt_cov_cpp.Rd man/cmpt_global_pca.Rd man/cmpt_loadings.Rd man/cmpt_local_pca.Rd man/cmpt_minor_af.Rd man/covRob_cpp.Rd man/create.pcadapt.Rd man/display.local.pca.Rd man/get.output.name.Rd man/get.pc.Rd man/get.pool.matrix.Rd man/get.pop.names.Rd man/get.score.color.Rd man/get_nb_ind.Rd man/get_pop_size.Rd man/get_size_cpp.Rd man/get_window.Rd man/impute.pcadapt.Rd man/impute_geno.Rd man/impute_geno_pop.Rd man/lfmm2pcadapt.Rd man/loc.anc.plotting.Rd man/lrfunc_cpp.Rd man/manhattan.plotting.Rd man/matrix_rsvd.Rd man/neutral.plotting.Rd man/pca_rotation.Rd man/pcadapt.Rd man/ped2pcadapt.Rd man/plot.pcadapt.Rd man/print_convert.Rd man/pvalqq.plotting.Rd man/rdadapt.Rd man/read.pcadapt.Rd man/residuals_to_stat.Rd man/run.pcadapt.Rd man/sample_geno_file.Rd man/sample_geno_matrix.Rd man/scale_geno.Rd man/scan.intro.Rd man/score.plotting.Rd man/scree.plotting.Rd man/slidingWindows_fast.Rd man/slidingWindows_new.Rd man/svd.pcadapt.Rd man/updt_local_scores.Rd man/vcf2pcadapt.Rd man/vcf_convert.Rd
pcadapt.Rproj
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/bedadapt.cpp
src/covariance.cpp
src/geometry.cpp
src/geometry.h
src/imputationUtils.cpp
src/introUtils.cpp
src/introUtils.h
src/matrix.cpp
src/ogk.cpp
src/pedUtils.cpp
src/poolUtils.cpp
src/sandbox.cpp
src/shape.cpp
src/toolbox.cpp
src/toolbox.h
src/vcfUtils.cpp
tests/testthat.R tests/testthat/test_cov.R tests/testthat/test_name.R tests/testthat/test_pool.R vignettes/pcadapt.R vignettes/pcadapt.Rmd
vignettes/pcadapt.html
vignettes/style.css
vignettes/tuto_data.Rmd vignettes/tuto_fdr.Rmd vignettes/tuto_introgression.Rmd vignettes/tuto_pca.Rmd
bcm-uga/pcadapt documentation built on Nov. 7, 2017, 8:16 a.m.