Files in privefl/bigsnpr
Analysis of Massive SNP Arrays

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/MAX3.R R/PRS.R R/RcppExports.R R/apply-parallelize.R R/autoSVD.R R/bigSNP-class.R R/bigsnpr.R R/binom-scaling.R R/corr.R R/external-software.R R/fake.R R/get-save-infos.R R/impute.R R/man-qq-gc.R R/pcadapt.R R/pruning.R R/readplink.R R/subset-QC.R R/utils-assert.R R/utils.R R/writeplink.R R/zzz.R README.md
_pkgdown.yml
appveyor.yml
bigsnpr.Rproj
cleanup
code_of_conduct.md cran-comments.md data-raw/long-range-LD-regions-wiki34.R
data/LD.wiki34.rda
docs/articles/demo.html
docs/articles/demo_files/figure-html/unnamed-chunk-3-1.png
docs/articles/demo_files/figure-html/unnamed-chunk-3-2.png
docs/articles/demo_files/figure-html/unnamed-chunk-3-3.png
docs/articles/demo_files/figure-html/unnamed-chunk-4-1.png
docs/articles/demo_files/figure-html/unnamed-chunk-4-2.png
docs/articles/demo_files/figure-html/unnamed-chunk-4-3.png
docs/articles/how-to-PCA.html
docs/articles/index.html
docs/articles/pruning-vs-clumping.html
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/reference/LD.wiki34.html
docs/reference/bigSNP-class.html
docs/reference/bigsnpr-package.html
docs/reference/download_beagle.html
docs/reference/download_plink.html
docs/reference/index.html
docs/reference/pruning-clumping.html
docs/reference/snp_MAF.html
docs/reference/snp_MAX3-4.png
docs/reference/snp_MAX3-5.png
docs/reference/snp_MAX3-6.png
docs/reference/snp_MAX3.html
docs/reference/snp_PRS-2.png
docs/reference/snp_PRS.html
docs/reference/snp_attach.html
docs/reference/snp_attachExtdata.html
docs/reference/snp_autoSVD.html
docs/reference/snp_beagleImpute.html
docs/reference/snp_cor.html
docs/reference/snp_fake.html
docs/reference/snp_fastImpute.html
docs/reference/snp_gc-4.png
docs/reference/snp_gc-5.png
docs/reference/snp_gc-6.png
docs/reference/snp_gc.html
docs/reference/snp_getSampleInfos.html
docs/reference/snp_manhattan-4.png
docs/reference/snp_manhattan-5.png
docs/reference/snp_manhattan-6.png
docs/reference/snp_manhattan.html
docs/reference/snp_pcadapt-3.png
docs/reference/snp_pcadapt-4.png
docs/reference/snp_pcadapt.html
docs/reference/snp_plinkIBDQC.html
docs/reference/snp_plinkQC.html
docs/reference/snp_plinkRmSamples.html
docs/reference/snp_qq-4.png
docs/reference/snp_qq-5.png
docs/reference/snp_qq-6.png
docs/reference/snp_qq.html
docs/reference/snp_readBed.html
docs/reference/snp_save.html
docs/reference/snp_scaleBinom-3.png
docs/reference/snp_scaleBinom-4.png
docs/reference/snp_scaleBinom.html
docs/reference/snp_split.html
docs/reference/snp_writeBed.html
docs/reference/subset.bigSNP.html
examples/example-PRS.R examples/example-man-qq-gc.R examples/example-pruning.R examples/example-readplink.R examples/example-save.R examples/example-writeplink.R
inst/CITATION
inst/WORDLIST
inst/extdata/cluster1
inst/extdata/cluster2
inst/extdata/cluster3
inst/extdata/example.bed
inst/extdata/example.bim
inst/extdata/example.fam
inst/extdata/example.genome
inst/extdata/example.log
inst/extdata/example.nosex
inst/testdata/clumping.rds
inst/testdata/example.ld
inst/testdata/pruning_ct.prune.in
inst/testdata/pruning_kb.prune.in
inst/testdata/pval.rds
inst/testdata/scores-PRS.rds
man/LD.wiki34.Rd man/bigSNP-class.Rd man/bigsnpr-package.Rd man/download_beagle.Rd man/download_plink.Rd man/pruning-clumping.Rd man/snp_MAF.Rd man/snp_MAX3.Rd man/snp_PRS.Rd man/snp_attach.Rd man/snp_attachExtdata.Rd man/snp_autoSVD.Rd man/snp_beagleImpute.Rd man/snp_cor.Rd man/snp_fake.Rd man/snp_fastImpute.Rd man/snp_gc.Rd man/snp_getSampleInfos.Rd man/snp_manhattan.Rd man/snp_pcadapt.Rd man/snp_plinkIBDQC.Rd man/snp_plinkQC.Rd man/snp_plinkRmSamples.Rd man/snp_qq.Rd man/snp_readBed.Rd man/snp_save.Rd man/snp_scaleBinom.Rd man/snp_split.Rd man/snp_writeBed.Rd man/subset.bigSNP.Rd
raw-vignettes/data/cluster_Finn_v2
raw-vignettes/data/cluster_IT
raw-vignettes/data/cluster_NL
raw-vignettes/data/cluster_UK1_v2
raw-vignettes/data/cluster_UK3_v2
raw-vignettes/how-to-PCA.Rmd
raw-vignettes/refs.bib
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/copy-subset.cpp
src/corr.cpp
src/pcadapt.cpp
src/pruning.cpp
src/readplink.cpp
src/rollmean.cpp
tests/spelling.R tests/testthat.R tests/testthat/test-MAX3.R tests/testthat/test-PRS.R tests/testthat/test-attach.R tests/testthat/test-corr.R tests/testthat/test-fake.R tests/testthat/test-fastImpute.R tests/testthat/test-get-save-infos.R tests/testthat/test-parallel.R tests/testthat/test-pcadapt.R tests/testthat/test-plink-QC.R tests/testthat/test-pruning.R tests/testthat/test-readBed.R tests/testthat/test-subset.R tests/testthat/test-writeBed.R tmp-save/bigsnpr.R
tmp-save/center.cpp
tmp-save/computeK_mloss.cpp
tmp-save/crossval.R tmp-save/double.R
tmp-save/double.cpp
tmp-save/getSNPinfos.R tmp-save/impute.R
tmp-save/local-clumping
tmp-save/mat-to-geno.R tmp-save/plink-PRS.R tmp-save/pruning.R
tmp-save/pruning.cpp
tmp-save/qcimpute.R
tmp-save/readplink
tmp-save/revert.cpp
tmp-save/test.counts.R
tmp-tests/IBS.cpp
tmp-tests/IRLS.R
tmp-tests/IRLS.cpp
tmp-tests/IRLS2.R tmp-tests/MAX3-celiac.R tmp-tests/benchmark-accessCols.R tmp-tests/copy-code.R tmp-tests/debug-pruning.R tmp-tests/debug-pruning2.R tmp-tests/expected-error.pdf tmp-tests/expected-error2.pdf tmp-tests/fisher.R
tmp-tests/fstream.cpp
tmp-tests/imputation-celiac.R tmp-tests/investigae-diff-impute.R tmp-tests/privefl.R
tmp-tests/raw-access.cpp
tmp-tests/readBedCpp.R tmp-tests/readBedParallel.R tmp-tests/readBedRaw.R tmp-tests/readBedVec.R tmp-tests/reprod-splt4.R
tmp-tests/reprod-splt4.html
tmp-tests/reprod.rds
tmp-tests/simus.R tmp-tests/test-GRM.R tmp-tests/test-GWAS-PRS.R tmp-tests/test-HiLMM.R tmp-tests/test-HiLMM2.R tmp-tests/test-IBS-missing.R tmp-tests/test-IBS.R
tmp-tests/test-IBS.cpp
tmp-tests/test-IBS2.R tmp-tests/test-IBS3.R tmp-tests/test-OGK.R tmp-tests/test-PCA-before-IBS.R
tmp-tests/test-T.cpp
tmp-tests/test-XGBoost-celiac.R tmp-tests/test-XGBoost-celiac2.R tmp-tests/test-XGBoost-celiac3.R tmp-tests/test-XGBoost-celiac4.R tmp-tests/test-XGBoost.R tmp-tests/test-XGBoost2.R tmp-tests/test-XGBoost3.R tmp-tests/test-XGBoost4.R tmp-tests/test-XGBoost5.R tmp-tests/test-XGBoost6.R tmp-tests/test-XGBoost7.R tmp-tests/test-adjust-PCA-R2.R
tmp-tests/test-ceil.cpp
tmp-tests/test-codeDosage.R tmp-tests/test-codeDosage2.R tmp-tests/test-corNA.R tmp-tests/test-cvPRS-fast.R tmp-tests/test-dist-nbNA-celiac.R tmp-tests/test-fa.Rmd tmp-tests/test-hetX.R tmp-tests/test-hmisc-pval.R tmp-tests/test-imputation-beagle.R tmp-tests/test-impute-popres.R tmp-tests/test-impute-popres2.R tmp-tests/test-impute.R tmp-tests/test-lambdaGC.R tmp-tests/test-manhattan.R tmp-tests/test-merge.R tmp-tests/test-new-clumping.R tmp-tests/test-newCounts.R tmp-tests/test-newRandomSVD_cpp.R tmp-tests/test-newRead.R tmp-tests/test-newSubset.R tmp-tests/test-order-parallel.R tmp-tests/test-pcadapt.R tmp-tests/test-pcadapt2.R tmp-tests/test-pcadapt3.R tmp-tests/test-plink-pruning.R
tmp-tests/test-plink-pruning.cpp
tmp-tests/test-plink-pruning2.R tmp-tests/test-plink-pruning3.R tmp-tests/test-popres-svd-thr.R tmp-tests/test-pruning.R tmp-tests/test-signif-between.R tmp-tests/test-tcrossprod-table.R
tmp-tests/test-tcrossprod-table.cpp
tmp-tests/test-triple-accessor.cpp
tmp-tests/test.cpp
tmp-tests/thoughts-raw-access.R tmp-tests/weigths.Rmd
tmp-tests/weigths.html
tmp-tests/writeBed.R tmp-tests/writeBed2.R tmp-tests/writeBed3.R vignettes/demo.Rmd
vignettes/how-to-PCA.html
vignettes/pruning-vs-clumping.Rmd
privefl/bigsnpr documentation built on Dec. 7, 2017, 12:10 p.m.