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

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/RcppExports.R R/bed2matrix.R R/hist-plot.R R/iram.R R/manhattan-plot.R R/pcadapt.R R/pcadaptRead.R R/pcadaptUtils.R R/plotUtils.R R/qq-plot.R R/score-plot.R R/scree-plot.R R/vcfConverter.R R/writebed.R README.md TODO.md
_pkgdown.yml
appveyor.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
docs/articles/pcadapt_files/figure-html/unnamed-chunk-16-1.png
docs/articles/pcadapt_files/figure-html/unnamed-chunk-17-1.png
docs/articles/pcadapt_files/figure-html/unnamed-chunk-18-1.png
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/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/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/lfmm2pcadapt.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
pcadapt-bcm.Rproj
pcadapt.Rproj
src/.gitignore
src/Makevars
src/Makevars.win
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/vcfUtils.cpp
src/writebed.cpp
tests/testthat.R tests/testthat/test_convert.R tests/testthat/test_missing.R tests/testthat/test_read.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/ogk.cpp
tmp-save/pcadapt.R
tmp-save/test.cpp
tmp-tests/COMPARE-BEFORE.R tmp-tests/Check_package_privefl.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 June 29, 2018, 11:38 a.m.