API for GenABEL
genome-wide SNP association analysis

Global functions
DISABLED.onAttach	Source code
GASurv	Man page
GenABEL	Man page
GenABEL-package	Man page
HWE.show	Man page
LiLog	Source code
PGC	Man page Source code
VIFGC	Man page Source code
VIFGC_ovdom	Man page Source code
Xfix	Man page
[,gwaa.data,ANY,ANY,ANY-method	Man page
[,scan.gwaa,ANY,ANY,ANY-method	Man page
[,snp.coding,ANY,missing,missing-method	Man page
[,snp.data,ANY,ANY,ANY-method	Man page
[,snp.mx,ANY,ANY,ANY-method	Man page
[,snp.strand,ANY,missing,missing-method	Man page
add.phdata	Man page
add.plot	Man page
alleleID.alleles	Source code
alleleID.char2raw	Source code
alleleID.codes	Source code
alleleID.codes.reverse	Source code
alleleID.effective	Source code
alleleID.raw2char	Source code
alleleID.raw2char.matrix	Source code
alleleID.reference	Source code
alleleID.revstrand	Source code
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 Source code
as.character.gwaa.data	Man page
as.character.snp.coding	Man page
as.character.snp.data	Man page Source code
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 Source code
catable	Man page
ccfast	Man page
check.marker	Man page
check.marker-class	Man page
check.trait	Man page
checkPackageVersionOnCRAN	Man page Source code
checkphengen	Source code
chi2_CG	Man page Source code
chrom.char2num	Source code
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,gwaa.data-method	Man page
coding,scan.gwaa-method	Man page
coding,snp.data-method	Man page
coding<-	Man page
coding<-,gwaa.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 Source code
descriptives.marker	Man page
descriptives.scan	Man page
descriptives.trait	Man page Source code
dim,scan.gwaa-method	Man page
dim,snp.data-method	Man page
dimnames,scan.gwaa-method	Man page
dimnames,snp.data-method	Man page
dprfast	Man page
dump.piece	Source code
dump.piece.New	Source code
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
estLambdaKS	Source code
estlambda	Man page
export.impute	Man page
export.merlin	Man page
export.plink	Man page
extract.annotation.impute	Man page Source code
extract.annotation.mach	Man page Source code
findRelatives	Man page Source code
formetascore	Man page
genabel	Man page
generateOffspring	Man page Source code
getLogLikelihoodGivenRelation	Man page Source code
getcall	Man page
getcall,scan.gwaa-method	Man page
getfamily	Man page
getfamily,scan.gwaa-method	Man page
grammar	Man page
gtdata	Man page
gtdata,gwaa.data-method	Man page
gwaa.data-class	Man page
hom	Man page
hom.old	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 Source code
impute2mach	Man page Source code
lambda	Man page
lambda,scan.gwaa-method	Man page
load.gwaa.data	Man page
lossFunctionLambdaKS	Source code
mach2databel	Man page Source code
makeTransitionMatrix	Man page Source code
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
minimac2databel	Source code
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
palinear2LiLog	Source code
patch_strand	Man page
perid.summary	Man page
phdata	Man page Source code
phdata,gwaa.data-method	Man page
phdata<-	Man page
phdata<-,gwaa.data-method	Man page
plot, check.marker-method	Man page
plot, scan.gwaa.2D-method	Man page
plot,scan.gwaa-method	Man page
plot.check.marker	Man page
plot.scan.gwaa	Man page
plot.scan.gwaa.2D	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 Source code
reconstructNPs	Man page Source code
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-class	Man page
scan.gwaa.2D-class	Man page
scan.haplo	Man page
scan.haplo.2D	Man page
show,gwaa.data-method	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
show.ncbi	Man page
snp.coding-class	Man page
snp.data	Man page Source code
snp.data-class	Man page
snp.mx-class	Man page
snp.names	Man page
snp.strand-class	Man page
snp.subset	Man page Source code
snpnames	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
sortmap.internal	Man page
sset	Man page
strand	Man page
strand,gwaa.data-method	Man page
strand,scan.gwaa-method	Man page
strand,snp.data-method	Man page
strand<-	Man page
strand<-,gwaa.data-method	Man page
strand<-,snp.data-method	Man page
summary, check.marker-method	Man page
summary,gwaa.data-method	Man page
summary,snp.data-method	Man page
summary,snp.mx-method	Man page
summary.check.marker	Man page
summary.gwaa.data	Man page
summary.scan.gwaa	Man page
summary.snp.data	Man page
summary.snp.data_old	Man page
translate_mono_coding	Source code
ztransform	Man page