Files in GenABEL
genome-wide SNP association analysis
TODO
inst
inst/exdata
inst/exdata/map.18
inst/exdata/chr18.raw
inst/exdata/phenos.18
inst/exdata/pedin.18
inst/doc
inst/doc/index.html
inst/doc/GenABEL-tutorial.pdf
inst/unitTests
inst/unitTests/reportSummary.txt
inst/unitTests/Makefile
inst/unitTests/runit.polylik.R
inst/unitTests/runit.descriptives.trait.R
inst/unitTests/runit.recodeChromosome.R
inst/unitTests/runit.impute2xxx.R
inst/unitTests/runit.convert.snp.ped.R
inst/unitTests/runit.sortmap.internal.R
inst/unitTests/runit.exports.R
inst/unitTests/runit.strandModify.R
inst/unitTests/report.html
inst/unitTests/report.txt
inst/unitTests/runit.qtscore.R
inst/unitTests/runit.mmscore.R
inst/unitTests/runit.merge.R
inst/unitTests/runit.impute2xxx_large.R
inst/unitTests/runit.polygenic.R
inst/unitTests/runit.iterator.R
inst/unitTests/runit.convert.snp.R
inst/unitTests/runit.mach2databel.R
inst/unitTests/shared_functions.R
inst/unitTests/runit.findRelatives.R
tests
tests/gatest.illu
tests/map.18
tests/gatest.map
tests/gatest.tfam
tests/test.mlinfo
tests/test.mldose
tests/test_markers
tests/gatest1.tped
tests/test_mmscore_results_revision_1321
tests/TEST10x15.geno
tests/gatest.ped
tests/gatest.phe
tests/test_phenos
tests/test.mlprob
tests/impute.sample5
tests/test_impute2databel.R.save
tests/big_data
tests/big_data/README
tests/gatest1.tfam
tests/pedin.18
tests/gatest.tped
tests/gatest1.phe
src
src/ctest.h
src/convert_snp_merlin.cpp
src/gwaa_data.cpp
src/AbstractMatrix_R.cpp
src/merge.snp.data.cpp
src/dometa.h
src/Makevars
src/RealHandlerWrapper.cpp
src/convert_snp_illumina.cpp
src/Chip.cpp
src/chinv2.cpp
src/AbstractMatrix.cpp
src/survS.h
src/survproto.h
src/Transposer.h
src/FileVector.cpp
src/fexact.c
src/mematriR.h
src/ReusableFileHandle.cpp
src/convert_snp_merlin_wslash.cpp
src/gwaautil.cpp
src/frutil.cpp
src/dautil.cpp
src/convert.snp.affymetrix.cpp
src/Rstuff.h
src/lm_gwaa.cpp
src/Chip.h
src/frversion.h
src/frutil.h
src/coxfit2.cpp
src/FileVector.h
src/Logger.h
src/mematrix.h
src/chsolve2.cpp
src/CastUtils.cpp
src/interactions_rare_recesive_alleles.cpp
src/reg1.h
src/dometa.cpp
src/gtps_container.cpp
src/dautil.h
src/ReusableFileHandle.h
src/FilteredMatrix.cpp
src/FilteredMatrix_R.cpp
src/dmatrix.cpp
src/mematri1.h
src/gwaa_cpp.h
src/iterator.cpp
src/const.h
src/interactions_rare_recesive_alleles.h
src/gwaa.c
src/iterator_functions.h
src/AbstractMatrix.h
src/CastUtils.h
src/reg1data.h
src/RealHandlerWrapper.h
src/Logger.cpp
src/convert_util.h
src/cholesky2.cpp
src/Transposer.cpp
src/iterator_functions.cpp
src/export_plink.cpp
src/export_plink.h
src/Makevars.win
src/convert_snp_tped.cpp
src/convert_util.cpp
src/iterator.h
src/gwaa_cpp.cpp
src/FilteredMatrix.h
src/gtps_container.h
NAMESPACE
demo
demo/ge03d2.R
demo/ge03d2ex.R
demo/00Index
demo/srdtawin.R
demo/srdta.R
R
R/extract.annotation.mach.R
R/HWE.show.R
R/save.gwaa.data.R
R/Xfix.R
R/snp.data.R
R/ss.R
R/ases.R
R/r2fast.R
R/GASurv.R
R/export.merlin.R
R/cocohet.R
R/save.snp.data.R
R/emp.mmscore.R
R/grammar.old.R
R/lilog.R
R/formetascore.R
R/rhofast.R
R/chi2_CG.R
R/perid.summary.R
R/check.marker.internal.R
R/scan.haplo.R
R/check.trait.R
R/refresh.gwaa.data.R
R/hom.old.R
R/patch_strand.R
R/plot.scan.gwaa.R
R/polylik.R
R/export.plink.R
R/sortmap.internal.R
R/descriptives.trait.R
R/descriptives.marker.R
R/GenABEL.R
R/dprfast.R
R/check.marker.R
R/summary.snp.data_old.R
R/generateOffspring.R
R/catable.R
R/ccfast.new.R
R/alleleID.R
R/qqplot.R
R/VIFGC_ovdom.R
R/convert.snp.illumina.R
R/blurGenotype.R
R/scan.glm.R
R/checkphengen.R
R/plot.check.marker.R
R/cross.R
R/egscore.R
R/update.check.marker.R
R/impute2mach.R
R/add.plot.R
R/summary.gwaa.data.R
R/autosomal.R
R/summary.check.marker.R
R/estlambda.R
R/merge.gwaa.data.R
R/PGC.R
R/egscore.old.R
R/getLogLikelihoodGivenRelation.R
R/fcc.R
R/npsubtreated.R
R/scan.glm.2D.R
R/Xcheck.R
R/plot.scan.gwaa.2D.R
R/phdata.R
R/qvaluebh95.R
R/convert.snp.mach.R
R/polygenic_hglm.R
R/redundant.R
R/convert.snp.tped.R
R/convert.snp.ped.R
R/recodeChromosome.R
R/formetascore_engage.R
R/grammar.R
R/load.gwaa.data.R
R/impute2databel.R
R/add.phdata.R
R/summary.scan.gwaa.R
R/put.snps.R
R/summary.snp.data.R
R/scan.haplo.2D.R
R/emp.ccfast.R
R/minimac2databel.R
R/makeTransitionMatrix.R
R/sset.R
R/snp.names.R
R/mmscore.R
R/mach2databel.R
R/findRelatives.R
R/show.ncbi.R
R/VIFGC.R
R/imphetcheck.R
R/metascore.R
R/mlreg.p.R
R/convert.snp.text.R
R/hom.R
R/guessType.R
R/crnames.R
R/ccfast.R
R/zUtil.R
R/fcc.new.R
R/r2fast.old.R
R/qtscore.R
R/descriptives.scan.R
R/arrange_probabel_phe.R
R/palinear2LiLog.R
R/export.impute.R
R/del.phdata.R
R/emp.qtscore.R
R/get_snp_plots.R
R/ibs.R
R/merge.snp.data.R
R/rntransform.R
R/polygenic.R
R/convert.snp.affymetrix.R
R/emp.grammar.R
R/checkPackageVersionOnCRAN.R
R/extract.annotation.impute.R
R/ibs.old.R
R/zzz.R
R/reconstructNPs.R
R/drop.out.points.R
R/ztransform.R
R/mlreg.R
R/snp.subset.R
MD5
DESCRIPTION
ChangeLog
man
man/scan.glm.Rd
man/GenABEL.Rd
man/ibs.old.Rd
man/scan.gwaa.2D-class.Rd
man/snp.names.Rd
man/snp.subset.Rd
man/egscore.Rd
man/export.merlin.Rd
man/mlreg.p.Rd
man/scan.glm.2D.Rd
man/descriptives.trait.Rd
man/summary.snp.data.Rd
man/snp.coding-class.Rd
man/qtscore.Rd
man/gwaa.data-class.Rd
man/check.marker.Rd
man/as.hsgeno.Rd
man/VIFGC_ovdom.Rd
man/r2fast.Rd
man/as.data.frame.gwaa.data.Rd
man/rntransform.Rd
man/add.plot.Rd
man/descriptives.marker.Rd
man/add.phdata.Rd
man/del.phdata.Rd
man/as.hsgeno.snp.data.Rd
man/npsubtreated.Rd
man/as.character.snp.strand.Rd
man/summary.gwaa.data.Rd
man/as.double.gwaa.data.Rd
man/estlambda.Rd
man/catable.Rd
man/sset.Rd
man/snp.strand-class.Rd
man/recodeChromosome.Rd
man/getLogLikelihoodGivenRelation.Rd
man/merge.snp.data.Rd
man/check.marker-class.Rd
man/show.ncbi.Rd
man/snp.mx-class.Rd
man/patch_strand.Rd
man/convert.snp.ped.Rd
man/convert.snp.text.Rd
man/rhofast.Rd
man/descriptives.scan.Rd
man/Xfix.Rd
man/impute2mach.Rd
man/export.plink.Rd
man/GASurv.Rd
man/as.genotype.gwaa.data.Rd
man/save.gwaa.data.Rd
man/extract.annotation.mach.Rd
man/autosomal.Rd
man/emp.qtscore.Rd
man/PGC.Rd
man/as.genotype.snp.data.Rd
man/scan.gwaa-class.Rd
man/impute2databel.Rd
man/polygenic.Rd
man/ccfast.Rd
man/reconstructNPs.Rd
man/merge.gwaa.data.Rd
man/makeTransitionMatrix.Rd
man/findRelatives.Rd
man/export.impute.Rd
man/as.genotype.Rd
man/dprfast.Rd
man/egscore.old.Rd
man/plot.scan.gwaa.Rd
man/ibs.Rd
man/as.double.snp.data.Rd
man/ztransform.Rd
man/summary.check.marker.Rd
man/as.character.gwaa.data.Rd
man/perid.summary.Rd
man/snp.data.Rd
man/load.gwaa.data.Rd
man/formetascore.Rd
man/r2fast.old.Rd
man/VIFGC.Rd
man/mmscore.Rd
man/redundant.Rd
man/convert.snp.illumina.Rd
man/plot.check.marker.Rd
man/sortmap.internal.Rd
man/summary.scan.gwaa.Rd
man/convert.snp.tped.Rd
man/mlreg.Rd
man/grammar.Rd
man/checkPackageVersionOnCRAN.Rd
man/convert.snp.affymetrix.Rd
man/as.character.snp.coding.Rd
man/qvaluebh95.Rd
man/snp.data-class.Rd
man/scan.haplo.Rd
man/hom.old.Rd
man/polygenic_hglm.Rd
man/extract.annotation.impute.Rd
man/convert.snp.mach.Rd
man/blurGenotype.Rd
man/generateOffspring.Rd
man/as.character.snp.data.Rd
man/mach2databel.Rd
man/arrange_probabel_phe.Rd
man/as.hsgeno.gwaa.data.Rd
man/crnames.Rd
man/check.trait.Rd
man/HWE.show.Rd
man/refresh.gwaa.data.Rd
man/emp.ccfast.Rd
man/cocohet.Rd
man/snps.cell-class.Rd
man/hom.Rd
man/plot.scan.gwaa.2D.Rd
man/scan.haplo.2D.Rd
