GenABEL: genome-wide SNP association analysis

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

Author
GenABEL project developers
Date of publication
2013-12-27 14:47:02
Maintainer
Yurii Aulchenko <yurii@bionet.nsc.ru>
License
GPL (>= 2)
Version
1.8-0
URLs

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