GenABEL: genome-wide SNP association analysis

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

Install the latest version of this package by entering the following in R:
install.packages("GenABEL")
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

Functions

add.phdata Man page
add.plot Man page
annotation Man page
annotation,gwaa.data-method Man page
annotation,scan.gwaa-method Man page
annotation,snp.data-method Man page
arrange_probabel_phe Man page
as.character.gwaa.data Man page
as.character.snp.coding Man page
as.character.snp.data Man page
as.character.snp.strand Man page
as.data.frame.gwaa.data Man page
as.double.gwaa.data Man page
as.double.snp.data Man page
as.genotype Man page
as.genotype.gwaa.data Man page
as.genotype.snp.data Man page
as.hsgeno Man page
as.hsgeno.gwaa.data Man page
as.hsgeno.snp.data Man page
autosomal Man page
blurGenotype Man page
catable Man page
ccfast Man page
check.marker Man page
check.marker-class Man page
checkPackageVersionOnCRAN Man page
check.trait Man page
chi2_CG Man page
chromosome Man page
chromosome,gwaa.data-method Man page
chromosome,scan.gwaa-method Man page
chromosome,snp.data-method Man page
cocohet Man page
coding Man page
coding<- Man page
coding<-,gwaa.data-method Man page
coding,gwaa.data-method Man page
coding,scan.gwaa-method Man page
coding<-,snp.data-method Man page
coding,snp.data-method Man page
coerce,snp.coding,character-method Man page
coerce,snp.data,character-method Man page
coerce,snp.data,genotype-method Man page
coerce,snp.data,hsgeno-method Man page
coerce,snp.data,numeric-method Man page
coerce,snp.mx,character-method Man page
coerce,snp.mx,numeric-method Man page
coerce,snp.strand,character-method Man page
convert.snp.affymetrix Man page
convert.snp.illumina Man page
convert.snp.mach Man page
convert.snp.ped Man page
convert.snp.text Man page
convert.snp.tped Man page
crnames Man page
del.phdata Man page
descriptives.marker Man page
descriptives.scan Man page
descriptives.trait Man page
dimnames,scan.gwaa-method Man page
dimnames,snp.data-method Man page
dim,scan.gwaa-method Man page
dim,snp.data-method Man page
dprfast Man page
effallele Man page
effallele,gwaa.data-method Man page
effallele,scan.gwaa-method Man page
effallele,snp.data-method Man page
egscore Man page
egscore.old Man page
emp.ccfast Man page
emp.qtscore Man page
estlambda Man page
export.impute Man page
export.merlin Man page
export.plink Man page
extract.annotation.impute Man page
extract.annotation.mach Man page
findRelatives Man page
formetascore Man page
GASurv Man page
genabel Man page
GenABEL Man page
GenABEL-package Man page
generateOffspring Man page
getcall Man page
getcall,scan.gwaa-method Man page
getfamily Man page
getfamily,scan.gwaa-method Man page
getLogLikelihoodGivenRelation Man page
grammar Man page
gtdata Man page
gtdata,gwaa.data-method Man page
[,gwaa.data,ANY,ANY,ANY-method Man page
gwaa.data-class Man page
hom Man page
hom.old Man page
HWE.show Man page
ibs Man page
ibs.old Man page
idnames Man page
idnames,gwaa.data-method Man page
idnames,scan.gwaa-method Man page
idnames,snp.data-method Man page
impute2databel Man page
impute2mach Man page
lambda Man page
lambda,scan.gwaa-method Man page
load.gwaa.data Man page
mach2databel Man page
makeTransitionMatrix Man page
male Man page
male,gwaa.data-method Man page
male,scan.gwaa-method Man page
male,snp.data-method Man page
map Man page
map,gwaa.data-method Man page
map,scan.gwaa-method Man page
map,snp.data-method Man page
merge.gwaa.data Man page
merge.snp.data Man page
mlreg Man page
mlreg.p Man page
mmscore Man page
nids Man page
nids,gwaa.data-method Man page
nids,scan.gwaa-method Man page
nids,snp.data-method Man page
npsubtreated Man page
nsnps Man page
nsnps,gwaa.data-method Man page
nsnps,scan.gwaa-method Man page
nsnps,snp.data-method Man page
patch_strand Man page
perid.summary Man page
PGC Man page
phdata Man page
phdata<- Man page
phdata<-,gwaa.data-method Man page
phdata,gwaa.data-method Man page
plot.check.marker Man page
plot, check.marker-method Man page
plot.scan.gwaa Man page
plot.scan.gwaa.2D Man page
plot, scan.gwaa.2D-method Man page
plot,scan.gwaa-method Man page
polygenic Man page
polygenic_hglm Man page
qtscore Man page
qvaluebh95 Man page
r2fast Man page
r2fast.old Man page
recodeChromosome Man page
reconstructNPs Man page
redundant Man page
refallele Man page
refallele,gwaa.data-method Man page
refallele,scan.gwaa-method Man page
refallele,snp.data-method Man page
refresh.gwaa.data Man page
reg.gwaa Man page
results Man page
results,scan.gwaa-method Man page
rhofast Man page
rntransform Man page
save.gwaa.data Man page
scan.glm Man page
scan.glm.2D Man page
scan.gwaa.2D-class Man page
[,scan.gwaa,ANY,ANY,ANY-method Man page
scan.gwaa-class Man page
scan.haplo Man page
scan.haplo.2D Man page
show,gwaa.data-method Man page
show.ncbi Man page
show,scan.gwaa-method Man page
show,snp.coding-method Man page
show,snp.data-method Man page
show,snp.mx-method Man page
show,snp.strand-method Man page
[,snp.coding,ANY,missing,missing-method Man page
snp.coding-class Man page
snp.data Man page
[,snp.data,ANY,ANY,ANY-method Man page
snp.data-class Man page
[,snp.mx,ANY,ANY,ANY-method Man page
snp.mx-class Man page
snpnames Man page
snp.names Man page
snpnames,gwaa.data-method Man page
snpnames,scan.gwaa-method Man page
snpnames,snp.data-method Man page
snps.cell-class Man page
[,snp.strand,ANY,missing,missing-method Man page
snp.strand-class Man page
snp.subset Man page
sortmap.internal Man page
sset Man page
strand Man page
strand<- Man page
strand<-,gwaa.data-method Man page
strand,gwaa.data-method Man page
strand,scan.gwaa-method Man page
strand<-,snp.data-method Man page
strand,snp.data-method Man page
summary.check.marker Man page
summary, check.marker-method Man page
summary.gwaa.data Man page
summary,gwaa.data-method Man page
summary.scan.gwaa Man page
summary.snp.data Man page
summary,snp.data-method Man page
summary.snp.data_old Man page
summary,snp.mx-method Man page
VIFGC Man page
VIFGC_ovdom Man page
Xfix Man page
ztransform Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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