[Genabel-commits] r2092 - in pkg: . GenABEL_indep GenABEL_indep/R GenABEL_indep/demo GenABEL_indep/inst GenABEL_indep/inst/doc GenABEL_indep/inst/exdata GenABEL_indep/inst/unitTests GenABEL_indep/man GenABEL_indep/src GenABEL_indep/tests GenABEL_indep/tests/big_data
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 19 18:45:59 CET 2022
Author: yurii
Date: 2022-01-19 18:45:59 +0100 (Wed, 19 Jan 2022)
New Revision: 2092
Added:
pkg/GenABEL_indep/
pkg/GenABEL_indep/ChangeLog
pkg/GenABEL_indep/DESCRIPTION
pkg/GenABEL_indep/LICENSE
pkg/GenABEL_indep/NAMESPACE
pkg/GenABEL_indep/R/
pkg/GenABEL_indep/R/GASurv.R
pkg/GenABEL_indep/R/GenABEL.R
pkg/GenABEL_indep/R/HWE.show.R
pkg/GenABEL_indep/R/PGC.R
pkg/GenABEL_indep/R/VIFGC.R
pkg/GenABEL_indep/R/VIFGC_ovdom.R
pkg/GenABEL_indep/R/Xcheck.R
pkg/GenABEL_indep/R/Xfix.R
pkg/GenABEL_indep/R/add.phdata.R
pkg/GenABEL_indep/R/add.plot.R
pkg/GenABEL_indep/R/alleleID.R
pkg/GenABEL_indep/R/arrange_probabel_phe.R
pkg/GenABEL_indep/R/ases.R
pkg/GenABEL_indep/R/autosomal.R
pkg/GenABEL_indep/R/blurGenotype.R
pkg/GenABEL_indep/R/catable.R
pkg/GenABEL_indep/R/ccfast.R
pkg/GenABEL_indep/R/ccfast.new.R
pkg/GenABEL_indep/R/check.marker.R
pkg/GenABEL_indep/R/check.marker.internal.R
pkg/GenABEL_indep/R/check.trait.R
pkg/GenABEL_indep/R/checkPackageVersionOnCRAN.R
pkg/GenABEL_indep/R/checkphengen.R
pkg/GenABEL_indep/R/chi2_CG.R
pkg/GenABEL_indep/R/cocohet.R
pkg/GenABEL_indep/R/convert.snp.affymetrix.R
pkg/GenABEL_indep/R/convert.snp.illumina.R
pkg/GenABEL_indep/R/convert.snp.mach.R
pkg/GenABEL_indep/R/convert.snp.ped.R
pkg/GenABEL_indep/R/convert.snp.text.R
pkg/GenABEL_indep/R/convert.snp.tped.R
pkg/GenABEL_indep/R/crnames.R
pkg/GenABEL_indep/R/cross.R
pkg/GenABEL_indep/R/del.phdata.R
pkg/GenABEL_indep/R/descriptives.marker.R
pkg/GenABEL_indep/R/descriptives.scan.R
pkg/GenABEL_indep/R/descriptives.trait.R
pkg/GenABEL_indep/R/dprfast.R
pkg/GenABEL_indep/R/drop.out.points.R
pkg/GenABEL_indep/R/egscore.R
pkg/GenABEL_indep/R/egscore.old.R
pkg/GenABEL_indep/R/emp.ccfast.R
pkg/GenABEL_indep/R/emp.grammar.R
pkg/GenABEL_indep/R/emp.mmscore.R
pkg/GenABEL_indep/R/emp.qtscore.R
pkg/GenABEL_indep/R/estlambda.R
pkg/GenABEL_indep/R/export.impute.R
pkg/GenABEL_indep/R/export.merlin.R
pkg/GenABEL_indep/R/export.plink.R
pkg/GenABEL_indep/R/extract.annotation.impute.R
pkg/GenABEL_indep/R/extract.annotation.mach.R
pkg/GenABEL_indep/R/fcc.R
pkg/GenABEL_indep/R/fcc.new.R
pkg/GenABEL_indep/R/findRelatives.R
pkg/GenABEL_indep/R/formetascore.R
pkg/GenABEL_indep/R/formetascore_engage.R
pkg/GenABEL_indep/R/generateOffspring.R
pkg/GenABEL_indep/R/getLogLikelihoodGivenRelation.R
pkg/GenABEL_indep/R/get_snp_plots.R
pkg/GenABEL_indep/R/grammar.R
pkg/GenABEL_indep/R/grammar.old.R
pkg/GenABEL_indep/R/guessType.R
pkg/GenABEL_indep/R/hom.R
pkg/GenABEL_indep/R/hom.old.R
pkg/GenABEL_indep/R/ibs.R
pkg/GenABEL_indep/R/ibs.old.R
pkg/GenABEL_indep/R/imphetcheck.R
pkg/GenABEL_indep/R/impute2databel.R
pkg/GenABEL_indep/R/impute2mach.R
pkg/GenABEL_indep/R/lilog.R
pkg/GenABEL_indep/R/load.gwaa.data.R
pkg/GenABEL_indep/R/mach2databel.R
pkg/GenABEL_indep/R/makeTransitionMatrix.R
pkg/GenABEL_indep/R/merge.gwaa.data.R
pkg/GenABEL_indep/R/merge.snp.data.R
pkg/GenABEL_indep/R/metascore.R
pkg/GenABEL_indep/R/minimac2databel.R
pkg/GenABEL_indep/R/mlreg.R
pkg/GenABEL_indep/R/mlreg.p.R
pkg/GenABEL_indep/R/mmscore.R
pkg/GenABEL_indep/R/npsubtreated.R
pkg/GenABEL_indep/R/palinear2LiLog.R
pkg/GenABEL_indep/R/patch_strand.R
pkg/GenABEL_indep/R/perid.summary.R
pkg/GenABEL_indep/R/phdata.R
pkg/GenABEL_indep/R/plot.check.marker.R
pkg/GenABEL_indep/R/plot.scan.gwaa.2D.R
pkg/GenABEL_indep/R/plot.scan.gwaa.R
pkg/GenABEL_indep/R/polygenic.R
pkg/GenABEL_indep/R/polygenic_hglm.R
pkg/GenABEL_indep/R/polylik.R
pkg/GenABEL_indep/R/put.snps.R
pkg/GenABEL_indep/R/qqplot.R
pkg/GenABEL_indep/R/qtscore.R
pkg/GenABEL_indep/R/qvaluebh95.R
pkg/GenABEL_indep/R/r2fast.R
pkg/GenABEL_indep/R/r2fast.old.R
pkg/GenABEL_indep/R/recodeChromosome.R
pkg/GenABEL_indep/R/reconstructNPs.R
pkg/GenABEL_indep/R/redundant.R
pkg/GenABEL_indep/R/refresh.gwaa.data.R
pkg/GenABEL_indep/R/rhofast.R
pkg/GenABEL_indep/R/rntransform.R
pkg/GenABEL_indep/R/save.gwaa.data.R
pkg/GenABEL_indep/R/save.snp.data.R
pkg/GenABEL_indep/R/scan.glm.2D.R
pkg/GenABEL_indep/R/scan.glm.R
pkg/GenABEL_indep/R/scan.haplo.2D.R
pkg/GenABEL_indep/R/scan.haplo.R
pkg/GenABEL_indep/R/show.ncbi.R
pkg/GenABEL_indep/R/snp.data.R
pkg/GenABEL_indep/R/snp.names.R
pkg/GenABEL_indep/R/snp.subset.R
pkg/GenABEL_indep/R/sortmap.internal.R
pkg/GenABEL_indep/R/ss.R
pkg/GenABEL_indep/R/sset.R
pkg/GenABEL_indep/R/summary.check.marker.R
pkg/GenABEL_indep/R/summary.gwaa.data.R
pkg/GenABEL_indep/R/summary.scan.gwaa.R
pkg/GenABEL_indep/R/summary.snp.data.R
pkg/GenABEL_indep/R/summary.snp.data_old.R
pkg/GenABEL_indep/R/update.check.marker.R
pkg/GenABEL_indep/R/zUtil.R
pkg/GenABEL_indep/R/ztransform.R
pkg/GenABEL_indep/R/zzz.R
pkg/GenABEL_indep/TODO
pkg/GenABEL_indep/demo/
pkg/GenABEL_indep/demo/00Index
pkg/GenABEL_indep/demo/ge03d2.R
pkg/GenABEL_indep/demo/ge03d2ex.R
pkg/GenABEL_indep/demo/srdta.R
pkg/GenABEL_indep/demo/srdtawin.R
pkg/GenABEL_indep/inst/
pkg/GenABEL_indep/inst/doc/
pkg/GenABEL_indep/inst/doc/index.html
pkg/GenABEL_indep/inst/exdata/
pkg/GenABEL_indep/inst/exdata/chr18.raw
pkg/GenABEL_indep/inst/exdata/map.18
pkg/GenABEL_indep/inst/exdata/pedin.18
pkg/GenABEL_indep/inst/exdata/phenos.18
pkg/GenABEL_indep/inst/unitTests/
pkg/GenABEL_indep/inst/unitTests/Makefile
pkg/GenABEL_indep/inst/unitTests/runit.convert.snp.R
pkg/GenABEL_indep/inst/unitTests/runit.convert.snp.ped.R
pkg/GenABEL_indep/inst/unitTests/runit.descriptives.trait.R
pkg/GenABEL_indep/inst/unitTests/runit.exports.R
pkg/GenABEL_indep/inst/unitTests/runit.findRelatives.R
pkg/GenABEL_indep/inst/unitTests/runit.impute2xxx.R
pkg/GenABEL_indep/inst/unitTests/runit.impute2xxx_large.R
pkg/GenABEL_indep/inst/unitTests/runit.iterator.R
pkg/GenABEL_indep/inst/unitTests/runit.mach2databel.R
pkg/GenABEL_indep/inst/unitTests/runit.merge.R
pkg/GenABEL_indep/inst/unitTests/runit.mmscore.R
pkg/GenABEL_indep/inst/unitTests/runit.polygenic.R
pkg/GenABEL_indep/inst/unitTests/runit.polylik.R
pkg/GenABEL_indep/inst/unitTests/runit.qtscore.R
pkg/GenABEL_indep/inst/unitTests/runit.recodeChromosome.R
pkg/GenABEL_indep/inst/unitTests/runit.sortmap.internal.R
pkg/GenABEL_indep/inst/unitTests/runit.strandModify.R
pkg/GenABEL_indep/inst/unitTests/shared_functions.R
pkg/GenABEL_indep/man/
pkg/GenABEL_indep/man/GASurv.Rd
pkg/GenABEL_indep/man/GenABEL.Rd
pkg/GenABEL_indep/man/HWE.show.Rd
pkg/GenABEL_indep/man/PGC.Rd
pkg/GenABEL_indep/man/VIFGC.Rd
pkg/GenABEL_indep/man/VIFGC_ovdom.Rd
pkg/GenABEL_indep/man/Xfix.Rd
pkg/GenABEL_indep/man/add.phdata.Rd
pkg/GenABEL_indep/man/add.plot.Rd
pkg/GenABEL_indep/man/arrange_probabel_phe.Rd
pkg/GenABEL_indep/man/as.character.gwaa.data.Rd
pkg/GenABEL_indep/man/as.character.snp.coding.Rd
pkg/GenABEL_indep/man/as.character.snp.data.Rd
pkg/GenABEL_indep/man/as.character.snp.strand.Rd
pkg/GenABEL_indep/man/as.data.frame.gwaa.data.Rd
pkg/GenABEL_indep/man/as.double.gwaa.data.Rd
pkg/GenABEL_indep/man/as.double.snp.data.Rd
pkg/GenABEL_indep/man/as.genotype.Rd
pkg/GenABEL_indep/man/as.genotype.gwaa.data.Rd
pkg/GenABEL_indep/man/as.genotype.snp.data.Rd
pkg/GenABEL_indep/man/as.hsgeno.Rd
pkg/GenABEL_indep/man/as.hsgeno.gwaa.data.Rd
pkg/GenABEL_indep/man/as.hsgeno.snp.data.Rd
pkg/GenABEL_indep/man/autosomal.Rd
pkg/GenABEL_indep/man/blurGenotype.Rd
pkg/GenABEL_indep/man/catable.Rd
pkg/GenABEL_indep/man/ccfast.Rd
pkg/GenABEL_indep/man/check.marker-class.Rd
pkg/GenABEL_indep/man/check.marker.Rd
pkg/GenABEL_indep/man/check.trait.Rd
pkg/GenABEL_indep/man/checkPackageVersionOnCRAN.Rd
pkg/GenABEL_indep/man/cocohet.Rd
pkg/GenABEL_indep/man/convert.snp.affymetrix.Rd
pkg/GenABEL_indep/man/convert.snp.illumina.Rd
pkg/GenABEL_indep/man/convert.snp.mach.Rd
pkg/GenABEL_indep/man/convert.snp.ped.Rd
pkg/GenABEL_indep/man/convert.snp.text.Rd
pkg/GenABEL_indep/man/convert.snp.tped.Rd
pkg/GenABEL_indep/man/crnames.Rd
pkg/GenABEL_indep/man/del.phdata.Rd
pkg/GenABEL_indep/man/descriptives.marker.Rd
pkg/GenABEL_indep/man/descriptives.scan.Rd
pkg/GenABEL_indep/man/descriptives.trait.Rd
pkg/GenABEL_indep/man/dprfast.Rd
pkg/GenABEL_indep/man/egscore.Rd
pkg/GenABEL_indep/man/egscore.old.Rd
pkg/GenABEL_indep/man/emp.ccfast.Rd
pkg/GenABEL_indep/man/emp.qtscore.Rd
pkg/GenABEL_indep/man/estlambda.Rd
pkg/GenABEL_indep/man/export.impute.Rd
pkg/GenABEL_indep/man/export.merlin.Rd
pkg/GenABEL_indep/man/export.plink.Rd
pkg/GenABEL_indep/man/extract.annotation.impute.Rd
pkg/GenABEL_indep/man/extract.annotation.mach.Rd
pkg/GenABEL_indep/man/findRelatives.Rd
pkg/GenABEL_indep/man/formetascore.Rd
pkg/GenABEL_indep/man/generateOffspring.Rd
pkg/GenABEL_indep/man/getLogLikelihoodGivenRelation.Rd
pkg/GenABEL_indep/man/grammar.Rd
pkg/GenABEL_indep/man/gwaa.data-class.Rd
pkg/GenABEL_indep/man/hom.Rd
pkg/GenABEL_indep/man/hom.old.Rd
pkg/GenABEL_indep/man/ibs.Rd
pkg/GenABEL_indep/man/ibs.old.Rd
pkg/GenABEL_indep/man/impute2databel.Rd
pkg/GenABEL_indep/man/impute2mach.Rd
pkg/GenABEL_indep/man/load.gwaa.data.Rd
pkg/GenABEL_indep/man/mach2databel.Rd
pkg/GenABEL_indep/man/makeTransitionMatrix.Rd
pkg/GenABEL_indep/man/merge.gwaa.data.Rd
pkg/GenABEL_indep/man/merge.snp.data.Rd
pkg/GenABEL_indep/man/mlreg.Rd
pkg/GenABEL_indep/man/mlreg.p.Rd
pkg/GenABEL_indep/man/mmscore.Rd
pkg/GenABEL_indep/man/npsubtreated.Rd
pkg/GenABEL_indep/man/patch_strand.Rd
pkg/GenABEL_indep/man/perid.summary.Rd
pkg/GenABEL_indep/man/plot.check.marker.Rd
pkg/GenABEL_indep/man/plot.scan.gwaa.2D.Rd
pkg/GenABEL_indep/man/plot.scan.gwaa.Rd
pkg/GenABEL_indep/man/polygenic.Rd
pkg/GenABEL_indep/man/polygenic_hglm.Rd
pkg/GenABEL_indep/man/qtscore.Rd
pkg/GenABEL_indep/man/qvaluebh95.Rd
pkg/GenABEL_indep/man/r2fast.Rd
pkg/GenABEL_indep/man/r2fast.old.Rd
pkg/GenABEL_indep/man/recodeChromosome.Rd
pkg/GenABEL_indep/man/reconstructNPs.Rd
pkg/GenABEL_indep/man/redundant.Rd
pkg/GenABEL_indep/man/refresh.gwaa.data.Rd
pkg/GenABEL_indep/man/rhofast.Rd
pkg/GenABEL_indep/man/rntransform.Rd
pkg/GenABEL_indep/man/save.gwaa.data.Rd
pkg/GenABEL_indep/man/scan.glm.2D.Rd
pkg/GenABEL_indep/man/scan.glm.Rd
pkg/GenABEL_indep/man/scan.gwaa-class.Rd
pkg/GenABEL_indep/man/scan.gwaa.2D-class.Rd
pkg/GenABEL_indep/man/scan.haplo.2D.Rd
pkg/GenABEL_indep/man/scan.haplo.Rd
pkg/GenABEL_indep/man/show.ncbi.Rd
pkg/GenABEL_indep/man/snp.coding-class.Rd
pkg/GenABEL_indep/man/snp.data-class.Rd
pkg/GenABEL_indep/man/snp.data.Rd
pkg/GenABEL_indep/man/snp.mx-class.Rd
pkg/GenABEL_indep/man/snp.names.Rd
pkg/GenABEL_indep/man/snp.strand-class.Rd
pkg/GenABEL_indep/man/snp.subset.Rd
pkg/GenABEL_indep/man/snps.cell-class.Rd
pkg/GenABEL_indep/man/sortmap.internal.Rd
pkg/GenABEL_indep/man/sset.Rd
pkg/GenABEL_indep/man/summary.check.marker.Rd
pkg/GenABEL_indep/man/summary.gwaa.data.Rd
pkg/GenABEL_indep/man/summary.scan.gwaa.Rd
pkg/GenABEL_indep/man/summary.snp.data.Rd
pkg/GenABEL_indep/man/ztransform.Rd
pkg/GenABEL_indep/src/
pkg/GenABEL_indep/src/AbstractMatrix.cpp
pkg/GenABEL_indep/src/AbstractMatrix.h
pkg/GenABEL_indep/src/AbstractMatrix_R.cpp
pkg/GenABEL_indep/src/CastUtils.cpp
pkg/GenABEL_indep/src/CastUtils.h
pkg/GenABEL_indep/src/Chip.cpp
pkg/GenABEL_indep/src/Chip.h
pkg/GenABEL_indep/src/FileVector.cpp
pkg/GenABEL_indep/src/FileVector.h
pkg/GenABEL_indep/src/FilteredMatrix.cpp
pkg/GenABEL_indep/src/FilteredMatrix.h
pkg/GenABEL_indep/src/FilteredMatrix_R.cpp
pkg/GenABEL_indep/src/Logger.cpp
pkg/GenABEL_indep/src/Logger.h
pkg/GenABEL_indep/src/Makevars
pkg/GenABEL_indep/src/Makevars.win
pkg/GenABEL_indep/src/RealHandlerWrapper.cpp
pkg/GenABEL_indep/src/RealHandlerWrapper.h
pkg/GenABEL_indep/src/ReusableFileHandle.cpp
pkg/GenABEL_indep/src/ReusableFileHandle.h
pkg/GenABEL_indep/src/Rstuff.h
pkg/GenABEL_indep/src/Transposer.cpp
pkg/GenABEL_indep/src/Transposer.h
pkg/GenABEL_indep/src/chinv2.cpp
pkg/GenABEL_indep/src/cholesky2.cpp
pkg/GenABEL_indep/src/chsolve2.cpp
pkg/GenABEL_indep/src/const.h
pkg/GenABEL_indep/src/convert.snp.affymetrix.cpp
pkg/GenABEL_indep/src/convert_snp_illumina.cpp
pkg/GenABEL_indep/src/convert_snp_merlin.cpp
pkg/GenABEL_indep/src/convert_snp_merlin_wslash.cpp
pkg/GenABEL_indep/src/convert_snp_tped.cpp
pkg/GenABEL_indep/src/convert_util.cpp
pkg/GenABEL_indep/src/convert_util.h
pkg/GenABEL_indep/src/coxfit2.cpp
pkg/GenABEL_indep/src/ctest.h
pkg/GenABEL_indep/src/dautil.cpp
pkg/GenABEL_indep/src/dautil.h
pkg/GenABEL_indep/src/dmatrix.cpp
pkg/GenABEL_indep/src/dometa.cpp
pkg/GenABEL_indep/src/dometa.h
pkg/GenABEL_indep/src/export_plink.cpp
pkg/GenABEL_indep/src/export_plink.h
pkg/GenABEL_indep/src/fexact.c
pkg/GenABEL_indep/src/frutil.cpp
pkg/GenABEL_indep/src/frutil.h
pkg/GenABEL_indep/src/frversion.h
pkg/GenABEL_indep/src/gtps_container.cpp
pkg/GenABEL_indep/src/gtps_container.h
pkg/GenABEL_indep/src/gwaa.c
pkg/GenABEL_indep/src/gwaa_cpp.cpp
pkg/GenABEL_indep/src/gwaa_cpp.h
pkg/GenABEL_indep/src/gwaa_data.cpp
pkg/GenABEL_indep/src/gwaautil.cpp
pkg/GenABEL_indep/src/interactions_rare_recesive_alleles.cpp
pkg/GenABEL_indep/src/interactions_rare_recesive_alleles.h
pkg/GenABEL_indep/src/iterator.cpp
pkg/GenABEL_indep/src/iterator.h
pkg/GenABEL_indep/src/iterator_functions.cpp
pkg/GenABEL_indep/src/iterator_functions.h
pkg/GenABEL_indep/src/lm_gwaa.cpp
pkg/GenABEL_indep/src/mematri1.h
pkg/GenABEL_indep/src/mematriR.h
pkg/GenABEL_indep/src/mematrix.h
pkg/GenABEL_indep/src/merge.snp.data.cpp
pkg/GenABEL_indep/src/reg1.h
pkg/GenABEL_indep/src/reg1data.h
pkg/GenABEL_indep/src/survS.h
pkg/GenABEL_indep/src/survproto.h
pkg/GenABEL_indep/tests/
pkg/GenABEL_indep/tests/TEST10x15.geno
pkg/GenABEL_indep/tests/big_data/
pkg/GenABEL_indep/tests/big_data/README
pkg/GenABEL_indep/tests/gatest.illu
pkg/GenABEL_indep/tests/gatest.map
pkg/GenABEL_indep/tests/gatest.ped
pkg/GenABEL_indep/tests/gatest.phe
pkg/GenABEL_indep/tests/gatest.tfam
pkg/GenABEL_indep/tests/gatest.tped
pkg/GenABEL_indep/tests/gatest1.phe
pkg/GenABEL_indep/tests/gatest1.tfam
pkg/GenABEL_indep/tests/gatest1.tped
pkg/GenABEL_indep/tests/impute.sample5
pkg/GenABEL_indep/tests/map.18
pkg/GenABEL_indep/tests/pedin.18
pkg/GenABEL_indep/tests/test.mldose
pkg/GenABEL_indep/tests/test.mlinfo
pkg/GenABEL_indep/tests/test.mlprob
pkg/GenABEL_indep/tests/test_impute2databel.R.save
pkg/GenABEL_indep/tests/test_markers
pkg/GenABEL_indep/tests/test_mmscore_results_revision_1321
pkg/GenABEL_indep/tests/test_phenos
Log:
adding GenABEL_indep as a new package
Added: pkg/GenABEL_indep/ChangeLog
===================================================================
--- pkg/GenABEL_indep/ChangeLog (rev 0)
+++ pkg/GenABEL_indep/ChangeLog 2022-01-19 17:45:59 UTC (rev 2092)
@@ -0,0 +1,1000 @@
+*** v.
+()
+- impute2databel() now accepts the option "snpfile", a file that contains
+ (short) SNP names. This is useful when using 1000 Genomes data with SNP
+ names that are (too) long for GenABEL/ProbABEL to handle. Thanks to
+ Matthias Wuttke for contributing this patch!
+- Fixed bug #6280: The convert.snp.affymetrix() function uses a
+ system("ls") call, which doesn't work on MS Windows. We now use R's
+ list.files() function, which is portable and works on all platforms.
+ Thanks to forum user Jrecoq for reporting this bug! (L.C. Karssen)
+- Fixed some spelling errors in the documentation.
+
+
+*** v. 1.8-0
+(2013.12.06)
+
+
+Fixed memory leak in a number of functions and deleted unused variables.
+Moved data objects ge03d2.clean, ge03d2c, ge03d2ex.clean, ge03d2ex,
+ge03d2 and srdta to a specially created new R package called
+GenABEL.data.
+
+*** v. 1.7-7
+(2013.11.04)
+Fixed bug #5040: Spelling of the name of G. Svischeva incorrect.
+
+(2013.08.27)
+Removed CRAN version checks following the request from B. Ripley,
+fixing other problems identified by --as-cran checks ("iterator"
+package changed from "DatABEL" to "GenABEL"; renaming CHANGES.LOG to
+ChangeLog), releasing this version on CRAN
+
+(2013.07.19)
+Added warning that *2databel's may not produce output in desired data type
+and fall onto float
+
+(2013.06.29)
+Changed the 'polygenic' nullification threshold to 1e-8
+
+Added references for Grammar+ transformation
+
+Allowed for user-specified output data type in '*2databel' functions
+
+Changed version number to 1.7-7
+
+(2013.06.06)
+Two new functions added: LiLog() and palinear2LiLog() for the
+estimation of logistic beta's from a linear regression. Thanks to
+Nicola Pirastu for this contribution. The paper that describes these
+methods has been submitted (see the help of both functions for the
+citation).
+
+(2013.06.03)
+Fixed bug #2664 in export.merlin() (exported files differ when using
+different settings for the stepids argument).
+
+(2013.05.30)
+Fixed memory leak in export.plink() when exporting to .ped format (Bug #2055).
+
+*** v. 1.7-6
+
+(2013.05.16)
+Negative eigenvalues set to 'very small' (1e-16) instead using abs
+in 'polygenic': this is more justified
+Fixed too long lines in Rd files.
+
+(2013.05.15)
+Updated version number to 1.7-6 (release), checked with latest
+dev-version of R available. Added 'bigRR' as suggested package.
+
+*** v. 1.7-5
+
+(2013.04.09)
+Fixing bug [#2672] (GenABEL::cocohet default graph output). Now by
+default the function does not produce graphics (makePlot = FALSE); if
+graphics is requested (makePlot = TRUE) it is produced using a default
+plot device (so a user can redirect the output to a file if (s)he
+desires and in the way (s)he desires).
+
+(2013.04.04)
+Fixing bug [#2525] (http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058)
+Thanks to Vladimir Naumov for submitting the patch!
+
+Updated documentation files
+
+(2013.04.03)
+Added patch to bug [#1287] - example(ibs) producing strange clusters.
+Thanks to Vladimir Naumov for submitting the patch!
+
+(2013.04.03)
+Upgraded the version number to 1.7-5
+
+(2013.04.02)
+Changed default behaviour of the export.plink() version. Export to .tped is now
+the default (because of the bugginess of the .ped export, see bug #2055.
+
+*** v. 1.7-4 (2013.02.22)
+
+(2013.02.22)
+replacing SNP with get("SNP") in impute2databel with option 'old' so to avoid
+CRAN checks complains
+
+(2013.02.03)
+Fixing bug in 'grammar': when using 'gamma', effects and s.e.s are not re-computed
+(bug reported by Xia Shen)
+
+(2013.01.18)
+Fixing bug in ztransform (if NA is present and formula used, NA's are kicked out)
+Changed the version number
+
+*** v. 1.7-3 (2013.01.09)
+
+(2013.01.09)
+Commented the parts related to non-additive GC in qtscore
+Removed calls to 'attach' from multiple procedures
+Decrease of running time for long-running examples
+(GC_ovdom,GC,check.marker,Xfix,srdta)
+
+(2013.01.07)
+Fixing the problem which prevents the package from loading while checking
+the version on CRAN
+
+(2012.12.03, YA)
+- Changes in DESCRIPTION and version to denote new working
+version
+- added argument 'eigenOfRel' to 'polygenic' allowing passing
+the results of 'eigen' of the relationship matrix instead of the matrix
+itself (makes much faster evaluation). See unit test test.polygenic.eigenOfRel
+for use example
+- found out that impute2databel is broken, see bug report [#2418]
+
+*** v. 1.7-2 (2012.10.14)
+
+(2012.09.14, YA)
+
+Changes in DESCRIPTION and version
+
+(2012.08.29, YA)
+
+Small changes related to CRAN release of 1.7-1; this release is to be
+updated to 1.7-2 as soon as the Grammar-Gamma paper is published and
+some feedback is collected for the 1.7-1
+
+(2012.08.15, YA)
+
+Small updates to documentation, verifying that checks are passed.
+Many NOTEs about use of partial arguments - something to fix
+eventually.
+
+(2012.08.09, YT)
+
+Add new function GC (Genomic control for non-additive models) and GC_ovdom
+fot overdominant model.
+Update some functions.
+
+(2012.07.06, YT)
+
+Removed documentation file grammar.old.Rd as obsolete
+Add new function PGC (Polynomial genomic control for non-additive models)
+
+*** v. 1.7-1 (2012.04.27)
+
+Replaced 'grammar' function with new one, allowing 'raw', 'gc'
+and 'gamma' varieties of the method.
+
+Added option weight = "eVar" to 'ibs'. This uses empirical variance of
+genotypes when estimating kinship matrix. This is useful when working with
+such data as Arabidopsis.
+
+*** v. 1.7-0 (2011.12.20)
+
+Addressed bug [#1383] (message about upgrade on loading the library
+not entirely correct) by adding new function checkPackageVersionOnCRAN()
+and re-writing zzz.R (.onLoad) using it.
+
+Addressed bug [#1673] (bug in load.gwaa.data and export.merlin when
+sorting is enabled, filed in by Daniel Taliun), added unit test
+runit.sortmap.internal.R/test.sortmap.internal.bug1673
+
+Addressed bug [#1676] (regression in merge of gwaa.data, phenotypes
+don't get merged correctly; filed in by Lennart Karssen), added unit
+test runit.merge.R/test.merge.bug1676
+
+Added 'KS' method to estimate lambda in 'estlambda'. Generates rather
+good results (under null) and may be considered as default option in the future,
+after testing under the alternative.
+
+Account for situation when HGLM fails to converge (s.e.'s set to NA in
+h2$h2an$se)
+
+added option 'transposed' to 'export.plink' to export TPED files
+
+speeding-up 'mmscore' by x1.8 through more efficient vector-matrix
+product computations
+
+export.merlin, export.plink now runs much faster (exports on C++ code)
+
+Bug [#1641] (regression bug with merge.snp.data in version 1.6.9;
+filed in by Karl Froner) fixed. Now GenABEL deals with exceptional
+situation in merge.snp.data / monomorphic part; added case of no overlap
+in SNPs (skip monomorphic stuff then). RUnit regression test
+runit.merge.R/test.merge.bug1641 added.
+
+Modifications in 'estlambda': plot=FALSE by default, added option
+to estimate Lambda with median method; added option 'filter' for
+filtering SNPs with 0-statistics
+
+*** v. 1.6-9 (2011.08.30)
+
+Change the name of 'maintainer' to genabel.project at gmail.com to avoid spamming
+CRAN people
+
+*** v. 1.6-8 (2011.08.25)
+
+added 'strand<-' method for snp.data and gwaa.daat-class
+
+added 'id' argument to 'load.gwaa.daat'. This may be handy when eg
+importing PLINK phenotypic data id="IID"
+
+Update of 'polygenic_hglm' by Xia Shen. Quote:
+We've updated the hglm package to version 1.2-2 recently on CRAN, where
+the major updates include:
+- Sparse matrix implementation
+- Multiple random effects
+- Function hglm2() which accepts lme4-style formula input
+In this update of polygenic_hglm() the speed could be slightly faster than
+before since the hglm() now uses sparse matrix technique (however I don't
+expect it to be much faster since the kinship matrix is always dense). Other
+modifications are:
+- The current update of hglm package does not spit out profile log-likelihood
+since we haven't perfectly solved the likelihood computation for multiple random
+effects yet. But since polygenic_hglm() only needs one random effect (polygenic
+effect), I've re-implemented the likelihood computation directly in
+polygenic_hglm(), and no need to specify 'method = "REML"' anymore.
+- In order to solve the problem from the forum about inputting formula as
+'y' or 'y ~ 1', I've added a check before creating the model.frame, so now
+ both types of inputs should work.
+
+Added 'recodeChromosome' function, which must be handy when e.g. importing data
+from other software which uses integer for sex chromosomes and other non-autosomes
+(X, Y, mt).
+
++> tutorial genetic data QC - list all options, do not use default?
+
+'check.marker' added "none" (equal to ibs.mrk = -1); set "both" to default
+
+Updated documentation for 'scan.glm.2D'.
+
+Added GRAMMAR+ transformation and computation of GRAMMAR+
+correction factors to 'polygenic'.
+
+The default value for the stand option to convert.snp.tped() is now "u",
+instead of "+". Now convert.snp.tped() and convert.snp.ped() have the
+same defaults.
+
+Added patch of bug [#1322] + regression test (contributed
+by Nicola Pirastu, see
+https://lists.r-forge.r-project.org/pipermail/genabel-devel/2011-May/000276.html).
+This is still suboptimal treatment -- the covariate is just dropped;
+in say 'lm' it is 'kept' with NA as estimate, and IDs with missing
+data dropped, which is not the case with 'polygenic'.
+
+Speeding up 'polygenic' by avoiding multiple inverses of
+the matrix.
+
+Fixed bug in 'polygenic' causing the offset in
+names(...$residualY) and names(...$pgresidualY) in
+case of missing observations.
+
+Updated the merge.snp.data procedure to allow meaningful
+merging of mono- and poly- codings. Take care -- this is
+new and not tested much yet! You best check few results
+manually after the merge!
+
+Added coding<- method to gwaa.data and snp.data classes
+
+Added I/D encoding and monomorphic classes (AA, TT, GG, CC,
+--, II, DD, ...) to 'snp.data' and convert.snp.*
+
+Updated 'polygenic' with use of 'polylik_eigen' developed by
+Gulnara Svischeva. Now 'polygenic' works MUCH faster. The
+main advantage of Gulnara's method is that time to compute
+the likelihood function is approximately linear with number
+of subjects. In that, relative speed-up grows with sample
+size growth, e.g. for 100 IDs, it is x15, x40 for 200,
+x60 for 400, and xX for 800 individuals (using two fixed effect
+covariates, see runit.polylik.R). Also added RUnit test to check
+consistency of results based on old 'polylik' and new
+'polylik_eigen'.
+
+Upgrade version number
+
+*** v. 1.6-7 (2011.05.17)
+
+Submitted 1.6-7, based on r727, to CRAN
+
+Deleting some pdf from 'doc' and compressing 'data'
+
+Fixed 'technical' bug [1398] (related to changes in R 2.14):
+https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1398&group_id=505&atid=2058
+
+Set 'GenABEL developers' as a maintainer of the package;
+set the genabel-devel list as 'maintainer' e-mail
+
+Fixing bug [1388], added regression test
+https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1388&group_id=505&atid=2058
+
+upgrade version number
+
+fix in example of polygenic_hglm
+
+*** v. 1.6-6 (2011.04.29)
+
+Added Xia Shen's procedure 'polygenic_hglm'. Features: quick
+convergence, standard errors for fixed effects.
+
+Updated check.marker, added warning if no. Y-markers is < 10
+
+Applied the patch of Nicola Pirastu
+http://lists.r-forge.r-project.org/pipermail/genabel-devel/2011-March/000182.html
+to descriptives.trait. Added RUnit regression tests, updated
+documentation. Bugs fixed: [#1184], [#1185], [#1259]
+
+Added 'reconstructNPs' function; added extra options
+to 'findRelatives'.
+
+Added a number of functions facilitating relationship checks.
+The core function is 'findRelatives'. Compared
+to guessing relations from genomic kinship matrix, this
+procedure offers several enhancements: (1) by use of IBD/IBS
+3-state space, it allows to distinguish between some pairs,
+which have the same kinship (e.g. parent-offspring from
+brother-sister; uncle-nephew from grandparent-grandchild, etc.)
+(2) it reports likelihood, allowing for more rigorous inferences
+
+Changes in convert.snp.mach documentation to reflect the fact that
+the map-file should have header; changes to convert.snp.illumina
+documentation to reflect the nature of the data better; added
+option 'mapHasHeaderLine' to convert.snp.ped and updated documentation
+(resolving feature request #1317).
+
+***** v. 1.6-5 (2011.02.07)
+
+Added '#include <cstdarg>' to iterator.cpp to solve
+'[#1273] GenABEL 1.6-5 does not compile'
+
+commented S4methods... in NAMESPACE to meet the
+request from the R-team; patched documentation for
+summary.scan.gwaa and summary.gwaa.data
+in order to avoid NOTE about S3methods "usage"
+section
+
+added extra checks for impute2databel to ensure that
+sample file header is not used
+
+change in merge.snp.data by Maksim Struchalin, adding option
+"intersected_snps_only" (if TRUE, then only interesected SNPs
+will be in output)
+
+Disabled check on intermediateXF in check.marker by setting intermediateXF=c(.5,.5)
+by default. This will be dealt with further (see tracker '[#1210] intermediate
+inbreeding checks with check.marker' )
+
+patched Roxygen documentation for qtscore
+
+use of 'setTxtProgressBar' in qtscore with times > 1 to indicate progress
+
+polygenic() added default option patchBasedOnFGLS, if no convergence based
+on difFGLS criterion, fixed effect betas are patched to FGLS betas before
+starting re-iteration
+
+adding a wrapper chi2_CG -> cocohet
+
+fixed 'demo(ge03d2)'
+
+'stepids' argument added to export.merlin
+
+Fan/Maksim's procedure for cocohet (CCH) procedure added, renamed by Yurii
+
+Bug fix in export.plink() thanks to Nadya Belonogova
+
+Made sure that SE reported does not carry the sign of beta (always 'abs')
+
+added mechanism to check for updates at load time
+
+moved summary.snp.data to 'iterator' framework, changes in gwaa.data at gtdata@gtps
+definition, now 'ANY' allowing for use of different types of data with
+interator. Interestingly, for 'old' data type computations became faster!
+
+
+***** v. 1.6-4 (2010.08.30)
+
+new official release tested by ESP29-2010 participants
+
+many thanks to everybody who provided feedback!
+
+***** v. 1.6-3 (2010.08.14)
+
+changes in the code and tutorial due to preparing
+for ESP29 course
+
+added function 'export.plink'
+
+added multiple methods to work with 'gwaa.data', 'snp.data' and
+'scan.gwaa classes, such as 'annotation', 'coding', 'refallele',
+'effallele', ...
+
+more annotations are delivered for summary objects
+
+***** v. 1.6-2 (2010.08.07)
+
+changes due to DatABEL functions names change
+
+***** v. 1.6-0 (2010.06.21)
+
+changes in DatABEL-embed functions used by impute2databel (treating of NAs);
+added tests for that situation
+
+***** v. 1.5-9 (2010.06.18)
+
+change in DESCRIPTION anyDuplicated() is in R 2.10.0, but not in 2.4.0
+
+small changes in polygenic -- convergence checks with intercept-only model; treatment
+for h2-boundary-stick situations (at small N)
+
+***** v. 1.5-8 (2010.06.10)
+
+multiple changes in polygenic default parameters
+and extra criteria now allowing better
+convergence. Many thanks to Nicola Pirastu for spotting
+poor convergence when multiple parameters were estimated!
+
+added methods "dim" and "dimnames" to snp.data-class
+
+***** v. 1.5-6 (2010.05.28)
+
+fixes in filevector
+
+Many thanks to Pau Navarro for help in identification of the bug!
+
+***** v. 1.5-4 (2010.05.09)
+
+changes in filevector related to DatABEL not passing checks on Windows
+(disconnect used FiltredMatrix destructor, which does not call
+AbstractMatrix destructor)
+
+***** v. 1.5-2 (2010.05.04)
+
+switching to new DatABEL with single class
+
+***** v. 1.5-1 (2010.03.17)
+
+further improvement and bug fixes in databel-facilitated functions
+
+***** v. 1.5-0 (2010.03.17)
+
+update of ABEL-tutorial (also few details on NCBI2R added)
+
+general clean-up, submission to CRAN
+
+extended add.phdata()
+
+added del.phdata(), shortcut to @male slot (function male())
+
+added checks for F in sex checks, ...$otherSexErr lists individuals with 0.2 > F > 0.8
+
+multiple changes to xxx2xxx (mach, impute, databel)
+
+***** v. 1.4-9 (2010.02.06)
+
+added arrange_probabel_phe(), also shortcuts to
+slots of gwaa.data-class: chromosome, coding,
+gtdata, idnames, map, nids, nsnps, phdata, snpnames, strand
+
+***** v. 1.4-8 (2010.01.24)
+
+added export.impute(), patch_strand(), mach2databel(), impute2databel(),
+impute2mach, extract.annotation.impute(), extract.annotation.mach()
+functions
+
+***** v. 1.4-7 (2009.12.03)
+
+cleaned help for polygenic()
+
+Diagonal elements returned by ibs(...,w="freq") changed from (0.5+F) to
+0.5*(1+F) (thanks to Chris Haley for pointing this problem out!)
+
+***** v. 1.4-6 (2009.11.06)
+
+Default formetascore's argument transform set to "no"
+
+***** v. 1.4-5 (2009.09.09)
+
+New function "var.meta" added.
+Function is intended for pooling (meta-analysing) trait means for
+different genotypes separately.Input files have to be like in example
+
+below (plink generate this kind of files). At the end you have one file
+in same format but with pooled MEANs and SDs
+
+***** v. 1.4-4 (2009.09.02)
+
+bug fix in hom() and perid.summary() -- only polymorphic markers were used to
+report call rate etc. Many thanks to Patrice Godard, who has reported the bug!
+The bug only appeared in version 1.4-3
+
+project submitted to r-forge
+
+***** v. 1.4-3 (2009.07.21)
+
+qvalue moved to "suggests"; no strict dependency on availability of that anymore
+(thanks to Beate Glaser for noting that tcltk is not so obvious component
+of all systems)
+
+changes to C++ LM code to improve portability (Solaris 10)
+
+hom() function updated, now producing variances (to be used as diagonal
+elements of the genomic kinshp matrix when doing EIGENSTRAT analysis).
+Many thanks to John Barnard for contributing the code!
+
+all class checks changed to ensure compatibility with S4
+(thanks to Maxime Rotival)
+
+
+***** v. 1.4-2b (2009.02.20)
+
+small fix in merge.gwaa.data (by="id")
+
+***** v. 1.4-2 (2009.01.28)
+
+Changes in polygenic()/mmscore() to allow for sub-setting on
+IDs
+
+Bug fix in mmscore(). The bug concernes estimates of beta, the
+P-values reported by mmscore() were not affected.
+
+***** v. 1.4-1 (2008.11.26)
+
+merge.gwaa.data, merge.snp.data well tested and
+recommended for wider use (special thanks to Arne
+Schillert and Michael Preuss)
+
+Modifications of some functions for better parallelizability.
+[user-invisible] changes to: ibs, hom, r2fast, perid.summary
+(thanks to Surakameth Mahasirimongkol and Unitsa Sangket)
+
+Resolved R 2.8.0 issues with load.gwaa.data.
+(thanks to many people reporting the problem)
+
+Partly resolving incompatibility between the way GenABEL
+computes the diagonal elemnts of the "covariance matrix"
+for use in egscore() and the original EIGENSTRAT matrix
+(many thanks to Guiseppe Palermo)
+
+***** v 1.4-0e (2008.09.18)
+
+Small changes in mlreg for consistency to formetascore required input
+
+Bug fix in mlreg (would produce meaningful results when no. snps is
+dividable by 4)
+
+***** v 1.4-0d (2008.08.21)
+
+bug fix in merge.snp.data() -- many thanks to Arne Schillert and Michael Preuss
+
+***** v 1.4-0c (2008.07.25)
+
+bug fix in estlambda() -- many thanks to Franz Quehenberger
+
+***** v 1.4-0b (2008.07.21)
+
+Multiple fixes in merge.snp.data
+
+Fix in check.marker (for Y-chromosome, the call rate
+was estimated using all people)
+
+
+***** v 1.3-9 (2008.04.23)
+
+Function mlreg() (aka reg.gwaa()) added. Implements maximum likelihood
+estimation and Wald test for linear and logistic regression and Cox
+proportional hazards models.
+
+Function convert.snp.affymetrix() added
+
+***** v 1.3-7 (2008.04.16)
+
+Function merge.gwaa.data() added
+
+Modifications to formetascore() (now can run with mmscore())
+
+Few cleanups
+
+***** v 1.3-6 (2008.03.20)
+
+Function merge.snp.data() added
+
+npsubtreated() updated with new functionality
+
+"quality" measure used in convert.snp.mach changed to 7th column (r2)
+
+plot.scan.gwaa(): option df="all" removed, options col, ystart added
+add.plot(): option colors added
+
+Improvement of formetascore function
+
+***** v 1.3-5c (2008.02.27)
+
+Bug fix in check.maker.internal (with "lower" option, would not exclude
+on IBS).
+
+Small bug fix estlambda (would not run if supplied with P-values, and
+some P-values are < 1.e-16). This bug did not affect any other function.
+
+***** v 1.3-5b (2008.02.21)
+
+Bug fix in ztransform(): would not work without data argument,
+if formula supplied will not use it. This bug also affected rntransform().
+
+***** v 1.3-5 (2008.02.15)
+
+qtscore "binomial" workout
+
+minor bug fix in check.marker() -- the procedure would fail to run
+in presence of more than couples of "twin" (e.g. multiple plant clones).
+
+bug fix in formetascore() function: standard errors were reported with
+sign of beta
+
+***** v 1.3-3d (2008.02.11)
+
+A fix in npsubtreated() function (in some situations all medicated
+people's values were set to NA)
+
+***** v 1.3-3c (2008.02.03)
+
+npsubtreated() function, to be used in analysis of
+traits affetcted by treatment (medication) added.
+
+formetascore() procedure extended with parameter "verbosity".
+
+***** v 1.3-3 (2008.01.12)
+
+autosomal() function added
+
+Y and mtDNA markers-specific analyses added in QC function check.marker()
+This also involves checks for people with XXY genotypes.
+
+Robust Genomic Control added to correct 2df test in qtscore
+function -- yet experimental.
+
+formetascore() function introduced -- analysis oriented to
+future meta-analysis.
+
+ztransform function created, rntransform function modified to take
+similar syntax as ztransform.
+
+Bug in convert.snp.merlin (similar to the one in convert.snp.illumina)
+fixed.
+
+***** v 1.3-2 (2007.12.18)
+
+Extensive cleanup, including fixes to mmscore and grammar;
+examples introduced for polygenic, mmscore, grammar, and others.
+
+Bug in convert.snp.tped (similar to the one in convert.snp.illumina)
+fixed.
+
+The number of people/genotypes (N) used in analysis of a particular SNP
+added to the output of qtscore, mmscore, ccfast, egscore, and grammar.
+
+plot.scan.gwaa changed -- now it is possible to use ylim.
+
+Bug fix in qtscore with binary traits without covariates -- there was
+no test whether coding is 0/1 (if not, test would be wrong).
+
+Changes in C code of concerns functions convert.snp.mach and
+convert.snp.ped. Speed of conversion from MACH format greatly
+improved.
+
+***** v 1.3-1 (2007.11.05)
+
+The strand information as based on build 35, is available from Yurii
+for Illumina 318K.
+
+Bug fix in convert.snp.illumina (alleles would change to the other one
+in large proportion of SNPs, e.g. A/G polymorphism, AA -> GG, GG -> AA).
+Though this does not affect results directly (e.g. P-values and the absolute
+effect values are OK), this may couse confusion when you compare your
+results to other people's results (the sign of the effect may be swapped),
+also imputations would have gone wrong.
+
+Small bug fixes with strand operations (SNP names were lost in sub-setting).
+
+New procedure rntransform(). This procedure performs
+rank transformation to normality. The transformed variable
+is perfectly normal, unless there are ties in the original
+distribution.
+
+***** v 1.2-9 (2007.10.22)
+
+A bug fix in check.markers(ibs.exclude="lower") -- before the fix, the
+samples with HIGHER call were excluded. Thanks to Tuuli Lappalainen!
+
+Bug fix in refresh.gwaa.data
+
+option "details" added to qtscore().
+When details=FALSE, SNP and ID names
+are not reported, which saves some memory
+
+***** v 1.2-8 (2007.08.27)
+
+GenABEL tutorial updated and, internals joined with
+tutorial, new introductory sections added.
+
+New association analysis procedure introduced.
+egscore() computes association statistics adjusted
+for eigenvector(s), following Price et al, Nat. Genet.,
+2006.
+
+Improved and new functionality of check.marker():
+much faster X-errors check, identification of female
+which are likely to be male. When "twin" DNAs are
+identified, the one with lower call may be dropped,
+or both (previously random).
+
+***** v 1.2-7 (2007.08.13)
+
+New list names added to output produced by qtscore(),
+grammar(), ccfast() and mmscore(): chi2.1df and
+chi2.2df. These correspond to Chi-square values produced.
+The minimal P-values, as before, are resti=ricted to 1e-16
+
+Improvements in plot.scan.gwaa() and add.plot() --
+now 0-probabilities converted to 1.e-16 (previously
+a warning message would be produced and the point would be
+dropped); also option df="Pc1df" introduced.
+
+***** v 1.2-6 (2007.08.08)
+
+A major improvement in GenABEL ability to import and export data
+compatible in format to other packages and databases.
+
+NOTE: to convert your R data from old to new format within R, use
+refresh.gwaa.data() function. Old phenotype- and genotype- files will load
+with load.gwaa.data with no problem.
+
+One of the main goals behind this effort was to make GW imputations
+with MACH software (G. Abecasis) easy.
+
+(a) New format of GenABEL data (0.1) developed. Now the
+ features stored by GenABEL include SNP coding (actual nucleotides)
+ and strand.
+
+(b) New and updated convert.snp.* functions, which convert genotypic
+ data from external to GenABEL format
+
+ -- convert.snp.ped: large improvement in speed (now in C++),
+ flexible control. Pre-makeped, MERLIN
+ and MACH formats supported
+
+ -- convert.snp.tped: some bug fixes, switch to 0.1 data format
+
+ -- convert.snp.mach (NEW!): converts MACH files to GenABEL
+ format, allowing for filtering on
+ quality
+
+ -- convert.snp.illumina (NEW!): converter for Affymetrix / Illumina
+ style of files
+
+(c) export.merlin() function to export data in MERLIN format. MACH
+ can be directly applied on these files. Coupled with
+ convert.snp.ped(format="mach") this allows easy data export,
+ imputations, and re-import.
+
+***** v 1.2-5 (2007.07.11)
+
+Some improvement of convert.snp.ped -- now is able to read
+alleles coded as characters
+
+***** v 1.2-4 (2007.07.10)
+
+Few small fixes done for compatibility with R 2.6.0-devel
+
+convert.snp.tped() procedure by Toby Johnson added.
+This procedure facilitates fast and effective conversion
+from PLINK TPED ("transposed pedigree") format to the
+GenABEL format. See help(convert.snp.tped).
+
+Few other small improvements. This is beta release version
+for procedures facilitating analyses using genomic
+kinship (IBD) matrix, such as polygenic(), mmscore() and
+grammar(). We tested these procedures with quantitative traits
+and they worked fine; for binary traits there may be few
+bugs yet.
+
+***** v 1.2-2 (2007.06.07)
+
+Improvement in polygenic() to ensure convergence, two
+optimisation methods are now allowed.
+
+"Formula" part in qtscore changed to more standard format
+(now one can use any terms allowed in glm, no CRSNP term
+needed).
+
+Bugs in grammar and mmscore fixed. Previous version tended
+to produse some very wrong results.
+
+Polygenic silightly modified (new output objects added).
+A fix in polygenic with covariates.
+
+Other bug fix in stratified analysis with X-chromosome.
+
+***** v 1.2-1 (2007.06.04)
+
+A set of new procedures to do analysis in samples of related
+individuals. They also can be used for analysis of samples
+with population staratification and cryptic relations.
+
+polygenic() provides means to estimate "heritability" and effects
+of covariates, in data having some correlation, as described by
+(genomic) kinship matrix.
+
+Mixed-model score test mmscore() added. This implements the test
+for association between the vector of phenotypes y and vector of genotypes
+g by computing
+
+((y-E[y]) Inverse[V] (g-E[g])^2/((g-E[g]) Inverse[V] (g-E[g])
+
+where Inverse[V] is the inverse of variance-covariance matrix
+and E[y] is expectation of the trait, as provided by polygenic().
+
+grammar() procedure implements fast variant of the above score test
+
+((y-E[y]) Inverse[V] (g-E[g])^2/((g-E[g]) (g-E[g])
+
+This statistics does not have chi-squared distribution, but becomes
+distributed so after GC (thus Pc1df are fine P-values to use)
+
+NOTE: grammar is still experimental.
+
+An error in qtscore, which led to using always only 2 strata
+(male/female) in analysis of X-chromosome fixed.
+
+***** v 1.2-0 (2007.04.17)
+
+Large improvement in the speed of the qvaluebh95() procedure.
+The time used to grow quadratic with the number of P-values to
+evaluate, now reduced to linear.
+
+ibs() procedure "freq" option is updated to provide weighted
+measure of genomic identity.
+
+dprfast() facilitating fast D' computations added. The results
+produced are not exacly the same with D's from LD/genetics.
+
+***** v 1.1-9 (2007.04.04)
+
+A procedure for fast r2 computations (r2fast()) added.
+It seems that this procedure results in r2s which are biased upward
+at small values, compared to r2s from LD/genetics.
+
+A procedure to estimate Morton-Collins rho added (rhofast())
+
+***** v 1.1-8 (2007.03.12)
+
+empirical derivation of GW significance is now embedded into
+qtscore/ccfast, emp.* are now serving as shortcuts to
+call these functions with argument times=100
+
+qtscore: changes to treat binomial variables (residuals from glm)
+
+Added new data sets: ge03d2, ge03d2c
+
+Added demo ge03d2; this ones shows extensive QC + how to deal
+with genetic stratification.
+
+***** v 1.1-7 (2007.03.05)
+
+In scan.haplo.2D procedure with simulate = TRUE change 0s -> 1/(N+1)
+
+add.plot.scan.gwaa() function changed to add.plot(), now delas with
+"scan.gwaa" and "scan.gwaa.2D" objects
+
+as.data.frame.gwaa.data which takes out @phdata part is arranged
+
+Fixed bug which made qtscore, ccfast and emp.* use phenotypes from
+the attached data frame, even when the data argument was supplied.
+For qtscore and emp.qtscore Formula now can be formulated as character
+and a formula.
+
+hom() function developed (previously heteroz; now is implemented in C)
+
+perid.summary() designed to produce average heterozygosity and call rate
+per person; this implied changes in check.marker() and summary.check.marker()
+
+ibs() function developed, this one extends to check.marker()
+
+A family of descriptives.* functions added: .marker, .trait, .scan
+
+Much improved genetic data QC (check.marker); new function Xfix()
+
+***** v 1.1-6 (2007.02.12)
+
+Improved memory managmenet. In particular, @chromosome slot is now
+stored as a factor.
+
+***** v 1.1-4 (2006.12.21)
+
+Due to accumulated changes, version number updated.
+
+Multiple improvements and fixes + catable() function
+
+***** v 1.1.3 (2006.11.12)
+
+scan.glm.2D and scan.haplo.2D functions added
+
+run.haplo.score.slide renamed to scan.haplo for consistency
+
+heteroz() added
+
+scan.gwaa-class is modified: effects are also returned.
+This led to modification of C code for fastcc, qtscore, R
+code for qtscore(), ccfast(), fcc(), emp.qtscore(), emp.ccfast(),
+scan.glm()
+
+improved memory management in functions ccfats(), emp.ccfast(),
+qtscore(), emp.qtscore(), summary()
+
+show.ncbi() added
+
+***** v 1.1.2
+
+scan.glm patched (it did not work with df=2 when a SNP had only 2 genotypes)
+
+minor fix in sub-setting of snp.data class
+
+ccfast, qtscore, scan.glm, emp.ccfast, emp.qtscore and plot.scan.gwaa are modified.
+Major change concerns ccfast and qtscore: now, 1-df and 2-df tests are
+computed simultaneously within the C functions.
+The class "scan.gwaa" now contains both 1- and 2-df P-values.
+This also addresses the point on TODO:
+
+2006.08.17 implement qtscore function with 2df
+
+Small fix in qtscore and ccfast (to act on 1 d.f. when # genotypic classes is 2)
+
+The function scan.gwaa removed as redundant
+
+qtscore now allows for analysis using strata (Cochran-Mantel-Haenszel)
+
+Added average/median chi2 to the "scan.gwaa" class (to be used for genomic
+control)
+
+TODO fixed:
+2006.10.11 q-value returned by qvaluebh95() is wrong
+
+emp.qtscore and emp.qtfast optimised (runs 3-10 times faster) by
+removing unnecessary checks and calling C function directly
+(instead of calling ccfast/qtscore)
+
+NAMESPACE introduced
+
+Update of documentation: now R CMD check passes all checks
+
+Formal class introduced for scan.gwaa-class
+
+demo(srdta): demo(srdtawin) is made by removing load-data from demo(srdta)
+because this may not work when there are no administrator's priviliges
+
+last modified 08.11.2006
+
+***** v 1.0.2
+
+Function scan.glm is introduced; this allows to scan for interactions in
+an easy way. This is essentially a modified scan.gwaa.
+
+New function to convert ped-files type of data to internal format,
+convert.snp.ped, was arranged
+
+Function add.plot.scan.gwaa was added
+
+Library "methods" loaded on start-up
+
+last modified 01.11.2006
+
+
+
+***** v. 1.0.1
+
+is resolving the issue of
+
+2006.07.20 need fast exact test for HWE, along the lines of fastcc,
+ as HWE.exact is too slow (Yurii)
+
+and
+
+2006.10.11 gwaa.data should be easily sub-settable -- now one
[TRUNCATED]
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