Files in privefl/mypack

Analysis of Massive SNP Arrays

.Rbuildignore

.gitattributes

.github/.gitignore

.github/workflows/check-standard.yaml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/Fst.R R/LDpred2.R R/MAX3.R R/PRS.R R/RcppExports.R R/SCT.R R/ancestry-summary.R R/apply-parallelize.R R/autoSVD.R R/bed-class.R R/bed-clumping.R R/bed-mat-acc.R R/bed-mult-vec.R R/bed-projectPCA.R R/bed-tcrossprodSelf.R R/bigSNP-class.R R/bigsnpr-package.R R/binom-scaling.R R/clumping.R R/corr.R R/external-software.R R/fake.R R/get-save-infos.R R/impute.R R/lassosum2.R R/ld-scores.R R/ldsc.R R/man-qq-gc.R R/match-alleles.R R/modify-positions.R R/pcadapt.R R/prod-bgen.R R/read-bgen.R R/read-plink.R R/simu-pheno.R R/split-LD.R R/subset-QC.R R/utils-assert.R R/utils.R R/write-plink.R README.md

_pkgdown.yml

bigsnpr.Rproj

cleanup

codecov.yml

data-raw/1000G-phase3-common-norel.R data-raw/bgen.R data-raw/example-missing.R data-raw/long-range-LD-regions-wiki34.R data-raw/public-data.R

data-raw/public-data.zip

data-raw/public-data2.R data-raw/public-data3.R

data-raw/public-data3.zip

data-raw/to-test-ldpred2.R data-raw/to-test-ldsc.R

data/LD.wiki34.rda

docs/404.html

docs/articles/LDpred2.html

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docs/articles/SCT_files/header-attrs/header-attrs.js

docs/articles/ancestry.html

docs/articles/ancestry_files/crosstalk/css/crosstalk.css

docs/articles/ancestry_files/crosstalk/js/crosstalk.js

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docs/articles/ancestry_files/datatables-binding/datatables.js

docs/articles/ancestry_files/datatables-css/datatables-crosstalk.css

docs/articles/ancestry_files/dt-core/css/jquery.dataTables.extra.css

docs/articles/ancestry_files/dt-core/css/jquery.dataTables.min.css

docs/articles/ancestry_files/dt-core/js/jquery.dataTables.min.js

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docs/articles/ancestry_files/header-attrs/header-attrs.js

docs/articles/ancestry_files/htmlwidgets/htmlwidgets.js

docs/articles/ancestry_files/jquery/LICENSE.txt

docs/articles/ancestry_files/jquery/jquery.min.js

docs/articles/ancestry_files/pagedtable/css/pagedtable.css

docs/articles/ancestry_files/pagedtable/js/pagedtable.js

docs/articles/bedpca.html

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docs/articles/pruning-vs-clumping_files/header-attrs-2.6/header-attrs.js

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docs/authors.html

docs/bootstrap-toc.css

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docs/docsearch.js

docs/index.html

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docs/news/index.html

docs/pkgdown.css

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docs/pkgdown.yml

docs/reference/LD.wiki34.html

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docs/reference/bed_scaleBinom.html

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docs/reference/bigSNP-class.html

docs/reference/bigsnpr-package.html

docs/reference/coef_to_liab.html

docs/reference/download_1000G.html

docs/reference/download_beagle.html

docs/reference/download_plink.html

docs/reference/index.html

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docs/reference/seq_log.html

docs/reference/snp_MAF.html

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docs/reference/snp_match.html

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docs/reference/snp_pcadapt.html

docs/reference/snp_plinkIBDQC.html

docs/reference/snp_plinkKINGQC.html

docs/reference/snp_plinkQC.html

docs/reference/snp_plinkRmSamples.html

docs/reference/snp_prodBGEN.html

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docs/sitemap.xml

examples/example-PRS.R examples/example-ancestry-summary.R examples/example-impute.R examples/example-man-qq-gc.R examples/example-match.R examples/example-readplink.R examples/example-save.R examples/example-split-LD.R examples/example-writeplink.R

inst/CITATION

inst/WORDLIST

inst/extdata/cluster1

inst/extdata/cluster2

inst/extdata/cluster3

inst/extdata/example-missing.bed

inst/extdata/example-missing.bim

inst/extdata/example-missing.fam

inst/extdata/example.bed

inst/extdata/example.bim

inst/extdata/example.fam

man/LD.wiki34.Rd man/LDpred2.Rd man/SCT.Rd man/bed-class.Rd man/bed-methods.Rd man/bed_MAF.Rd man/bed_counts.Rd man/bed_cprodVec.Rd man/bed_prodVec.Rd man/bed_projectPCA.Rd man/bed_projectSelfPCA.Rd man/bed_randomSVD.Rd man/bed_scaleBinom.Rd man/bed_tcrossprodSelf.Rd man/bigSNP-class.Rd man/bigsnpr-package.Rd man/coef_to_liab.Rd man/download_1000G.Rd man/download_beagle.Rd man/download_plink.Rd man/reexports.Rd man/same_ref.Rd man/seq_log.Rd man/snp_MAF.Rd man/snp_MAX3.Rd man/snp_PRS.Rd man/snp_ancestry_summary.Rd man/snp_asGeneticPos.Rd man/snp_asGeneticPos2.Rd man/snp_attach.Rd man/snp_attachExtdata.Rd man/snp_autoSVD.Rd man/snp_beagleImpute.Rd man/snp_clumping.Rd man/snp_codes.Rd man/snp_cor.Rd man/snp_fake.Rd man/snp_fastImpute.Rd man/snp_fastImputeSimple.Rd man/snp_fst.Rd man/snp_gc.Rd man/snp_getSampleInfos.Rd man/snp_lassosum2.Rd man/snp_ld_scores.Rd man/snp_ldsc.Rd man/snp_ldsplit.Rd man/snp_manhattan.Rd man/snp_match.Rd man/snp_modifyBuild.Rd man/snp_pcadapt.Rd man/snp_plinkIBDQC.Rd man/snp_plinkKINGQC.Rd man/snp_plinkQC.Rd man/snp_plinkRmSamples.Rd man/snp_prodBGEN.Rd man/snp_qq.Rd man/snp_readBGEN.Rd man/snp_readBGI.Rd man/snp_readBed.Rd man/snp_save.Rd man/snp_scaleBinom.Rd man/snp_simuPheno.Rd man/snp_split.Rd man/snp_subset.Rd man/snp_thr_correct.Rd man/snp_writeBed.Rd man/sub-bed-ANY-ANY-ANY-method.Rd man/sub_bed.Rd raw-vignettes/bedpca.Rmd

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/RcppExports.cpp

src/bed-acc-xptr.cpp

src/bed-acc.h

src/bed-fun.cpp

src/bed-mat-acc.cpp

src/bed-prod-vec.cpp

src/clumping-bed.cpp

src/clumping-cached.cpp

src/clumping-utils.h

src/clumping.cpp

src/colstats.cpp

src/copy-subset.cpp

src/corr.cpp

src/corr_with_cov.cpp

src/fstream.h

src/impute-simple.cpp

src/lassosum2.cpp

src/ld-scores-sfbm.cpp

src/ld-scores.cpp

src/ldpred2-auto.cpp

src/ldpred2-sampling.cpp

src/ldpred2.cpp

src/multLinReg.cpp

src/optim-MLE-alpha.h

src/prod-bgen.cpp

src/read-bgen.cpp

src/read-plink.cpp

src/sp-colsumssq-sym.cpp

src/split-LD.cpp

src/write-plink.cpp

tests/spelling.R tests/testthat.R tests/testthat/helper-init.R tests/testthat/test-1-attach.R tests/testthat/test-1-fake.R tests/testthat/test-1-get-save-infos.R tests/testthat/test-1-prodBGEN.R tests/testthat/test-1-readBGEN.R tests/testthat/test-1-readBed.R tests/testthat/test-1-subset.R tests/testthat/test-1-writeBed.R tests/testthat/test-2-autoSVD.R tests/testthat/test-2-bed-clumping-SVD.R tests/testthat/test-2-corr.R tests/testthat/test-2-ld-scores.R tests/testthat/test-2-pca-project.R tests/testthat/test-3-fastImpute.R tests/testthat/test-3-plink-QC.R tests/testthat/test-4-MAX3.R tests/testthat/test-4-manhattan.R tests/testthat/test-4-pcadapt.R tests/testthat/test-4-split-LD.R tests/testthat/test-5-bed-prod-vec.R tests/testthat/test-5-match.R tests/testthat/test-5-parallel.R tests/testthat/test-6-PRS.R tests/testthat/test-6-SCT.R tests/testthat/test-7-OpenMP.R tests/testthat/test-8-LDpred2.R tests/testthat/test-8-simu-pheno.R tests/testthat/test-9-Fst.R tests/testthat/test-9-LDSC.R tests/testthat/test-9-lassosum2.R

tests/testthat/testdata/before_readonly.bk

tests/testthat/testdata/before_readonly.rds

tests/testthat/testdata/bgen_dosages.rds

tests/testthat/testdata/bgen_example.rds

tests/testthat/testdata/bgen_variants.rds

tests/testthat/testdata/bgen_varinfo.rds

tests/testthat/testdata/bgi_example.rds

tests/testthat/testdata/clumping.rds

tests/testthat/testdata/example.ld

tests/testthat/testdata/pval.rds

tests/testthat/testdata/scores-PRS.rds

tests/testthat/testdata/spMat.rds

tests/testthat/testdata/split_before.rds

tmp-save/assoc-bgen.R

tmp-save/assoc-bgen.cpp

tmp-save/avx2.cpp

tmp-save/bed-acc.h

tmp-save/bench-ld-scores.R tmp-save/bigsnpr.R

tmp-save/center.cpp

tmp-save/computeK_mloss.cpp

tmp-save/crossval.R

tmp-save/dgTMatrix-to-list.cpp

tmp-save/docker-ubsan

tmp-save/dosage.Rmd tmp-save/double.R

tmp-save/double.cpp

tmp-save/gene.R tmp-save/getSNPinfos.R tmp-save/impute.R tmp-save/impute2.R tmp-save/install-tinytex.R tmp-save/lassosum2-with-auto.R

tmp-save/ldpred2-auto-parallel.cpp

tmp-save/ldpred2-auto-with-list.cpp

tmp-save/ldsc-febrile-seizure.R

tmp-save/local-clumping

tmp-save/mat-to-geno.R

tmp-save/pcadapt-bed.cpp

tmp-save/plink-PRS.R tmp-save/power-calc.R tmp-save/pruning.R

tmp-save/pruning.cpp

tmp-save/public-data.R tmp-save/qcimpute.R

tmp-save/read-bgen.cpp

tmp-save/read-plink.cpp

tmp-save/read_bgen.R

tmp-save/readplink

tmp-save/revert.cpp

tmp-save/rhub-checks.R tmp-save/robLOF.R tmp-save/split-LD.R

tmp-save/split-LD.cpp

tmp-save/test-4-assocBGEN.R

tmp-save/test-coverage.yaml

tmp-save/test-gene.R 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/SCT.R tmp-tests/bed-corNA.R

tmp-tests/bed-wcor.cpp

tmp-tests/bench-PRIMME.R tmp-tests/bench-PRIMME2.R tmp-tests/bench-PRIMME3.R tmp-tests/bench-bed-parallel.R tmp-tests/bench-bed-row-count-openmp.R tmp-tests/bench-clumping-parallel.R tmp-tests/bench-clumping-parallel2.R tmp-tests/bench-clumping-parallel3.R tmp-tests/bench-clumping-parallel4.R tmp-tests/bench-corr-parallel.R tmp-tests/bench-grid-clump-parallel.R tmp-tests/bench-gsubfn.R tmp-tests/bench-impute-parallel.R tmp-tests/bench-kNN.R tmp-tests/bench-ldpred2.R tmp-tests/bench-new-update-ldpred2.R tmp-tests/bench-readplink.R

tmp-tests/bench-readplink2.cpp

tmp-tests/bench-readplink3.R tmp-tests/bench-snp_cor.R tmp-tests/bench-sparsematrix-index1.R tmp-tests/bench-spmat-corr.R tmp-tests/bench-subset.R tmp-tests/benchmark-accessCols.R tmp-tests/code-hdpca.R tmp-tests/copy-code.R tmp-tests/crash-large-SFBM-windows.R tmp-tests/debug-pruning.R tmp-tests/debug-pruning2.R tmp-tests/expected-error.pdf tmp-tests/expected-error2.pdf tmp-tests/faster-PRS-grid-update.R tmp-tests/fisher.R

tmp-tests/fstream.cpp

tmp-tests/imputation-celiac.R tmp-tests/investigae-diff-impute.R tmp-tests/investigate-ld.R

tmp-tests/kNN.cpp

tmp-tests/ldpred-ldsc.R tmp-tests/ldpred1.R tmp-tests/ldpred2.R tmp-tests/loadings-and-ldscores.Rmd tmp-tests/make-blocks.R tmp-tests/pop-subsample.R tmp-tests/privefl.R

tmp-tests/proto-MLE-optim-C++.cpp

tmp-tests/proto-MLE-optim-better.R

tmp-tests/proto-MLE-uniroot

tmp-tests/proto-ldpred.R tmp-tests/pruning-plink.R

tmp-tests/qbld-rgig.cpp

tmp-tests/raw-access.cpp

tmp-tests/rcpp-replaceNA.cpp

tmp-tests/rcpp-sample-prob012.cpp

tmp-tests/read-bgen-chi2.cpp

tmp-tests/read-bgen.R tmp-tests/read-gz-file.R

tmp-tests/read-gz-file.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/snp_hwe.cpp

tmp-tests/split-LD.cpp

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-LDGM.R tmp-tests/test-LDpred-precision.R tmp-tests/test-LedoitWolf-shrinkage.R tmp-tests/test-OGK.R tmp-tests/test-PCA-before-IBS.R tmp-tests/test-R2-liability.R tmp-tests/test-SVD-missing.R tmp-tests/test-SVD-missing3.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-add-more-blocks.R tmp-tests/test-add-more-blocks2.R tmp-tests/test-add-more-blocks3.R tmp-tests/test-adjust-PCA-R2.R tmp-tests/test-auto-postp.R

tmp-tests/test-bed-acc.cpp

tmp-tests/test-bgen-crash.R tmp-tests/test-boot-MLE.R tmp-tests/test-cached-clumping.R tmp-tests/test-causal-in-LD.R

tmp-tests/test-ceil.cpp

tmp-tests/test-clumping-bed.R

tmp-tests/test-clumping-parallel.cpp

tmp-tests/test-clumping.R tmp-tests/test-codeDosage.R tmp-tests/test-codeDosage2.R tmp-tests/test-conv-diagn.R tmp-tests/test-conv-diagn2.R tmp-tests/test-cor-maha-dist.R tmp-tests/test-corNA.R tmp-tests/test-corNA2.R tmp-tests/test-correct-LD.R tmp-tests/test-cvPRS-fast.R tmp-tests/test-dist-nbNA-celiac.R tmp-tests/test-downdating.R tmp-tests/test-fa.Rmd tmp-tests/test-fast-kNN.R tmp-tests/test-future.R tmp-tests/test-gen-cor.R tmp-tests/test-gen-cor2.R tmp-tests/test-gen-cor3.R tmp-tests/test-get-LD.R tmp-tests/test-get-LD2.R tmp-tests/test-get-LD3.R tmp-tests/test-get-LD4.R tmp-tests/test-get-LD5.R tmp-tests/test-get-LD6.R tmp-tests/test-get-LD7.R tmp-tests/test-get-LD8.R tmp-tests/test-get-LD9.R

tmp-tests/test-get-code.cpp

tmp-tests/test-getL.cpp

tmp-tests/test-glasso.R

tmp-tests/test-glasso.cpp

tmp-tests/test-glasso2.R

tmp-tests/test-glasso2.cpp

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-ss.R tmp-tests/test-impute.R tmp-tests/test-impute3.R tmp-tests/test-inv-corr.R tmp-tests/test-lambdaGC.R tmp-tests/test-lassosum2-2.R tmp-tests/test-lassosum2-3.R tmp-tests/test-lassosum2.R

tmp-tests/test-lassosum2.cpp

tmp-tests/test-ldpred-VI.R tmp-tests/test-ldpred-approx.R tmp-tests/test-ldpred-approx2.R tmp-tests/test-ldpred-auto-sparse.R tmp-tests/test-ldpred-chr6-auto-multiple.R tmp-tests/test-ldpred-chr6-auto.R tmp-tests/test-ldpred-chr6-multiple2.R tmp-tests/test-ldpred-chr6-multiple3.R tmp-tests/test-ldpred-chr6-multiple4.R tmp-tests/test-ldpred-chr6.R

tmp-tests/test-ldpred-cpp-postp.cpp

tmp-tests/test-ldpred-cpp-postp2.cpp

tmp-tests/test-ldpred-cpp-postp3.cpp

tmp-tests/test-ldpred-cpp.R

tmp-tests/test-ldpred-cpp.cpp

tmp-tests/test-ldpred-gibbs-approx.R tmp-tests/test-ldpred-prio.R tmp-tests/test-ldpred-prop-and-size.R tmp-tests/test-ldpred-prop-and-size2.R tmp-tests/test-ldpred-sparse.R tmp-tests/test-ldpred-whole-genome.R tmp-tests/test-ldpred2-alpha.R

tmp-tests/test-ldpred2-auto-alpha.cpp

tmp-tests/test-ldpred2-impl.R tmp-tests/test-ldpred2-varyN.R tmp-tests/test-liftOver2.R tmp-tests/test-liftOver3.R tmp-tests/test-liftOverPlink.R tmp-tests/test-linear-solver.R

tmp-tests/test-linear-solver.cpp

tmp-tests/test-linear-solver2.cpp

tmp-tests/test-linear-solver3.cpp

tmp-tests/test-locfdr.R tmp-tests/test-locfdr2.R tmp-tests/test-lots-iter.R tmp-tests/test-manhattan.R tmp-tests/test-merge.R tmp-tests/test-mixsqp.R tmp-tests/test-nearPD.R tmp-tests/test-new-autoSVD.R tmp-tests/test-new-autoSVD2.R tmp-tests/test-new-autoSVD3.R tmp-tests/test-new-autoSVD4.R tmp-tests/test-new-bed-fun.R tmp-tests/test-new-clumping.R tmp-tests/test-new-split.R tmp-tests/test-new-split2.R

tmp-tests/test-new-split2.cpp

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-outlier-pcadapt.R tmp-tests/test-outlier-sample.R tmp-tests/test-parallel-clumping.R

tmp-tests/test-parallel-clumping.cpp

tmp-tests/test-pca-1000G.R tmp-tests/test-pcadapt.R tmp-tests/test-pcadapt2.R tmp-tests/test-pcadapt3.R tmp-tests/test-pcadapt4-missing.R tmp-tests/test-pcadapt4.R tmp-tests/test-pcadapt5.R tmp-tests/test-plink-pca.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-prioPCA.R tmp-tests/test-project-PCA.R tmp-tests/test-project-PCA2.R tmp-tests/test-project-PCA3.R tmp-tests/test-prscs.R

tmp-tests/test-prscs.cpp

tmp-tests/test-pruning.R

tmp-tests/test-qapSA.cpp

tmp-tests/test-qapSA2.cpp

tmp-tests/test-r2-2.R tmp-tests/test-r2-3.R tmp-tests/test-r2-tuto.R tmp-tests/test-r2.R tmp-tests/test-random-access.R

tmp-tests/test-random-access.cpp

tmp-tests/test-rbeta.cpp

tmp-tests/test-rcpp-parallel.cpp

tmp-tests/test-rcpp-parallel2.cpp

tmp-tests/test-rcpp-parallel3.cpp

tmp-tests/test-read-bed-mmap.R

tmp-tests/test-read-bed-mmap.cpp

tmp-tests/test-regul-mix.R tmp-tests/test-reorder.R

tmp-tests/test-reorder.cpp

tmp-tests/test-reorder2.R

tmp-tests/test-reorder2.cpp

tmp-tests/test-reorder3.cpp

tmp-tests/test-rgamma-cpp.cpp

tmp-tests/test-rng-parallel.cpp

tmp-tests/test-robLOF.R

tmp-tests/test-rollmean.cpp

tmp-tests/test-signif-between.R tmp-tests/test-simple-impute.R

tmp-tests/test-solver.cpp

tmp-tests/test-sp-solver.cpp

tmp-tests/test-spMat.cpp

tmp-tests/test-spMat2.cpp

tmp-tests/test-sparsification.R tmp-tests/test-tcrossprod-table.R

tmp-tests/test-tcrossprod-table.cpp

tmp-tests/test-triple-accessor.cpp

tmp-tests/test-variant-of-LOF.R tmp-tests/test-vectorized-gibbs-loop.R tmp-tests/test-very-large-effect.R

tmp-tests/test-warn-Rcpp.cpp

tmp-tests/test-xgboost-Capi.cpp

tmp-tests/test-xgboost.cpp

tmp-tests/test-zlib.cpp

tmp-tests/test.cpp

tmp-tests/thoughts-raw-access.R tmp-tests/try-PRIMME.R tmp-tests/try-PRIMME2.R tmp-tests/try-better-bdiag-sym.R

tmp-tests/uniroot.cpp

tmp-tests/weigths.Rmd

tmp-tests/weigths.html

tmp-tests/writeBed.R tmp-tests/writeBed2.R tmp-tests/writeBed3.R vignettes/LDpred2.Rmd vignettes/SCT.Rmd vignettes/ancestry.Rmd vignettes/demo.Rmd vignettes/exo.Rmd

vignettes/how-to-PCA.html

vignettes/prs_uncertainty.Rmd vignettes/pruning-vs-clumping.Rmd

privefl/mypack documentation built on April 20, 2024, 1:51 a.m.