GASurv                  Makes survival data object for reg.gwaa
GenABEL                 GWAS in R
HWE.show                show HWE tables
PGC                     Polynomial genomic control
VIFGC                   Genomic control for various model of
                        inheritance using VIF
VIFGC_ovdom             Genomic control for over-dominant model of
                        inheritance using VIF
Xfix                    function to set impossible genotypes as missing
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"
check.trait             function to do primitive trait quality control
checkPackageVersionOnCRAN
                        checks what is the version of package on CRAN
cocohet                 Test for compound heterozygote effects
convert.snp.affymetrix
                        function to convert genotypic data from
                        Affymetrix to internal format
convert.snp.illumina    function to convert genotypic data from
                        Illumina/Affymetrix to internal format
convert.snp.mach        function to convert genotypic data from MACH
                        format to internal data format
convert.snp.ped         function to convert genotypic data in pedigree
                        fromat (+map) to internal data format
convert.snp.text        function to convert integer genotypic data file
                        to raw internal data formated file
convert.snp.tped        function to convert genotypic data in
                        transposed-ped format (.tped and .tfam) to
                        internal genotypic data formatted file
crnames                 Return column and row names
del.phdata              delete phenotypes from phdata
descriptives.marker     Function to generate descriptive summary tables
                        for genotypic data
descriptives.scan       Function to describe "top" hits in GWA scan
descriptives.trait      Function to generate descriptive summary tables
                        for phenotypic data
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 meta-analysis
generateOffspring       simulates offspring's genotypes
getLogLikelihoodGivenRelation
                        computes logLik of two blurGenotypes
grammar                 GRAMMAR test for association in samples with
                        genetic structure
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
ibs                     Computes (average) Idenity-by-State for a set
                        of people and markers
ibs.old                 Computes (average) Idenity-by-State for a set
                        of people and markers
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 SNP data
mlreg.p                 EXPERIMENTAL Linear and logistic regression and
                        Cox models for genome-wide SNP data
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
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 glm
scan.gwaa-class         Class "scan.gwaa"
scan.gwaa.2D-class      Class "scan.gwaa.2D"
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
snp.strand-class        Class "snp.strand"
snp.subset              function to subset objects of class scan.gwaa
                        and check.marker
snps.cell-class         Class "snps.cell"
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
ztransform              Transformation to standard Normal
