GenABEL: genome-wide SNP association analysis

a package for genome-wide association analysis between quantitative or binary traits and single-nucleotide polymorphisms (SNPs).

AuthorGenABEL project developers
Date of publication2013-12-27 14:47:02
MaintainerYurii Aulchenko <yurii@bionet.nsc.ru>
LicenseGPL (>= 2)
Version1.8-0
http://www.genabel.org
http://forum.genabel.org, http://genabel.r-forge.r-project.org/

View on CRAN

Man pages

add.phdata: Adds phenotypic variables to gwaa.data object

add.plot: function to plot additional GWAA results

arrange_probabel_phe: arranges ProbABEL phenotype-file

as.character.gwaa.data: Attempts to convert genotypic part of gwaa.data to character

as.character.snp.coding: Attempts to convert internal snp.coding-class to character

as.character.snp.data: Attempts to convert snp.data to character

as.character.snp.strand: Attempts to convert internal strand-class to character

as.data.frame.gwaa.data: Attempts to convert snp.data to "hsgeno"

as.double.gwaa.data: Attempts to convert gwaa.data to double

as.double.snp.data: Attempts to convert snp.data to double

as.genotype: Attempts to convert object to "genotype"

as.genotype.gwaa.data: Attempts to convert gwaa.data to "genotype"

as.genotype.snp.data: Attempts to convert snp.data to "genotype"

as.hsgeno: Attempts to convert object to "hsgeno"

as.hsgeno.gwaa.data: Attempts to convert gwaa.data to "hsgeno"

as.hsgeno.snp.data: Attempts to convert snp.data to "hsgeno"

autosomal: Function telling all autosomal SNPs

blurGenotype: blur genotype calls into probabilites

catable: function to generate summary table for quantitative data

ccfast: fast case-control analysis

check.marker: function to do genotypic quality control

check.marker-class: Class "check.marker"

checkPackageVersionOnCRAN: checks what is the version of package on CRAN

check.trait: function to do primitive trait quality control

cocohet: Test for compound heterozygote effects

convert.snp.affymetrix: function to convert genotypic data from Affymetrix to...

convert.snp.illumina: function to convert genotypic data from Illumina/Affymetrix...

convert.snp.mach: function to convert genotypic data from MACH format to...

convert.snp.ped: function to convert genotypic data in pedigree fromat (+map)...

convert.snp.text: function to convert integer genotypic data file to raw...

convert.snp.tped: function to convert genotypic data in transposed-ped format...

crnames: Return column and row names

del.phdata: delete phenotypes from phdata

descriptives.marker: Function to generate descriptive summary tables for genotypic...

descriptives.scan: Function to describe "top" hits in GWA scan

descriptives.trait: Function to generate descriptive summary tables for...

dprfast: Estimates D' between multiple markers

egscore: Fast score test for association, corrected with PC

egscore.old: Fast score test for association, corrected with PC

emp.ccfast: Genome-wide significance for a case-control GWA scan

emp.qtscore: Genome-wide significance for a GWA scan

estlambda: Estimate the inflation factor for a distribution of P-values

export.impute: function to export GenABEL data in IMPUTE format

export.merlin: function to export GenABEL data in merlin format

export.plink: Export GenABEL data in PLINK format

extract.annotation.impute: extracts SNP annotation from IMPUTE files

extract.annotation.mach: extracts SNP annotation from MACH/HapMap legend files

findRelatives: guesses relations between individuals

formetascore: function to run GWA analysis oriented for future...

GASurv: Makes survival data object for reg.gwaa

GenABEL: GWAS in R

generateOffspring: simulates offspring's genotypes

getLogLikelihoodGivenRelation: computes logLik of two blurGenotypes

grammar: GRAMMAR test for association in samples with genetic...

gwaa.data-class: Class "gwaa.data"

hom: function to compute average homozygosity within a person

hom.old: function to compute average homozygosity within a person

HWE.show: show HWE tables

ibs: Computes (average) Idenity-by-State for a set of people and...

ibs.old: Computes (average) Idenity-by-State for a set of people and...

impute2databel: converts IMPUTE-imputed files to DatABEL (filevector) format

impute2mach: converts IMPUTE to MACH files

load.gwaa.data: function to load GWAA data

mach2databel: converts MACH-imputed files to DatABEL (filevector) format

makeTransitionMatrix: Genotype transition probabilities matrices

merge.gwaa.data: function to merge objects of gwaa.data-class

merge.snp.data: function to merge objects of snp.data-class

mlreg: Linear and logistic regression and Cox models for genome-wide...

mlreg.p: EXPERIMENTAL Linear and logistic regression and Cox models...

mmscore: Score test for association in related people

npsubtreated: non-parametric trait "imputations" in treated people

patch_strand: function to change strand

perid.summary: Summary of marker data per person

PGC: Polynomial genomic control

plot.check.marker: plots "check.marker" object

plot.scan.gwaa: function to plot GWAA results

plot.scan.gwaa.2D: function to plot 2D scan results

polygenic: Estimation of polygenic model

polygenic_hglm: Estimation of polygenic model

qtscore: Fast score test for association

qvaluebh95: Computes Benjamini-Hochberg (95) q-value

r2fast: Estimates r2 between multiple markers

r2fast.old: Estimates r2 between multiple markers

recodeChromosome: Change chromosomal coding

reconstructNPs: reconstruct nuclear families

redundant: function to do redundancy check

refresh.gwaa.data: Updates an object from old to new GenABEL format

rhofast: Estimates rho between multiple markers

rntransform: Rank-transformation to normality

save.gwaa.data: function to save gwaa.data object

scan.glm: Scan GWA data using glm

scan.glm.2D: Scans regional data allowing for gene-gene interaction using...

scan.gwaa.2D-class: Class "scan.gwaa.2D"

scan.gwaa-class: Class "scan.gwaa"

scan.haplo: scan.haplo

scan.haplo.2D: runs haplo.score.slide with all pairs of markers in a region

show.ncbi: Shows the region on NCBI map

snp.coding-class: Class "snp.coding"

snp.data: creates an snp.data object

snp.data-class: Class "snp.data"

snp.mx-class: Class "snp.mx"

snp.names: extracts names of SNPs in a region

snps.cell-class: Class "snps.cell"

snp.strand-class: Class "snp.strand"

snp.subset: function to subset objects of class scan.gwaa and...

sortmap.internal: Internal function for map-sorting

sset: Internal use function for class snp.mx-class

summary.check.marker: Summary of check.marker object

summary.gwaa.data: function to summarise GWAA data

summary.scan.gwaa: Shortcut to 'descriptives...

summary.snp.data: function to summary GWAA data

VIFGC: Genomic control for various model of inheritance using VIF

VIFGC_ovdom: Genomic control for over-dominant model of inheritance using...

Xfix: function to set impossible genotypes as missing

ztransform: Transformation to standard Normal

Files in this package

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

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