Files in bigsnpr

Analysis of Massive SNP Arrays

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

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

src/corr_with_cov.cpp

src/Makevars

src/multLinReg.cpp

src/sp-colsumssq-sym.cpp

src/clumping-utils.h

src/bed-acc.h

src/ldpred2-sampling.cpp

src/RcppExports.cpp

src/read-plink.cpp

src/bed-prod-vec.cpp

src/ld-scores.cpp

src/bed-acc-xptr.cpp

src/write-plink.cpp

src/lassosum2.cpp

src/clumping.cpp

src/split-LD.cpp

src/fstream.h

src/ld-scores-sfbm.cpp

src/impute-simple.cpp

src/copy-subset.cpp

src/clumping-cached.cpp

src/clumping-bed.cpp

src/bed-mat-acc.cpp

src/ldpred2-auto.cpp

src/optim-MLE-alpha.h

src/prod-bgen.cpp

src/colstats.cpp

src/read-bgen.cpp

src/ldpred2.cpp

src/corr.cpp

src/bed-fun.cpp

inst/CITATION

inst/WORDLIST

inst/extdata/example-missing.fam

inst/extdata/cluster3

inst/extdata/example.fam

inst/extdata/example-missing.bed

inst/extdata/cluster1

inst/extdata/example.bim

inst/extdata/example-missing.bim

inst/extdata/example.bed

inst/extdata/cluster2

build/partial.rdb

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

tests/testthat/testdata/spMat.rds

tests/testthat/testdata/bgen_variants.rds

tests/testthat/testdata/bgen_example.rds

tests/testthat/testdata/clumping.rds

tests/testthat/testdata/before_readonly.rds

tests/testthat/testdata/bgen_dosages.rds

tests/testthat/testdata/split_before.rds

tests/testthat/testdata/before_readonly.bk

tests/testthat/testdata/bgen_varinfo.rds

tests/testthat/testdata/scores-PRS.rds

tests/testthat/testdata/example.ld

tests/testthat/testdata/pval.rds

tests/testthat/testdata/bgi_example.rds

data/LD.wiki34.rda

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

bigsnpr documentation built on March 31, 2023, 10:37 p.m.