add1KG2SampleGDS        Add the genotype information for the list of
                        pruned SNVs into the Profile GDS file
addBlockFromDetFile     Append information associated to ld blocks, as
                        indexes, into the Population Reference SNV
                        Annotation GDS file
addGeneBlockGDSRefAnnot
                        Append information associated to blocks, as
                        indexes, into the Population Reference SNV
                        Annotation GDS file
addGeneBlockRefAnnot    Append information associated to blocks, as
                        indexes, into the Population Reference SNV
                        Annotation GDS file
addRef2GDS1KG           Add the information about the unrelated
                        patients to the Reference GDS file
addStudy1Kg             Append information about the 1KG samples into
                        the Profile GDS file
computeAncestryFromSynthetic
                        Select the optimal K and D parameters using the
                        synthetic data and infer the ancestry of a
                        specific profile
computeAncestryFromSyntheticFile
                        Select the optimal K and D parameters using the
                        synthetic data and infer the ancestry of a
                        specific profile
computeKNNRefSample     Run a k-nearest neighbors analysis on one
                        specific profile
computeKNNRefSynthetic
                        Run a k-nearest neighbors analysis on a subset
                        of the synthetic dataset
computePCAMultiSynthetic
                        Project synthetic profiles onto existing
                        principal component axes generated using the
                        reference 1KG profiles
computePCARefSample     Project specified profile onto PCA axes
                        generated using known reference profiles
computePoolSyntheticAncestryGr
                        Run a PCA analysis and a K-nearest neighbors
                        analysis on a small set of synthetic data using
                        all 1KG profiles except the ones used to
                        generate the synthetic profiles
computeSyntheticROC     Calculate the AUROC of the inferences for
                        specific values of D and K using the inferred
                        ancestry results from the synthetic profiles.
createAUROCGraph        Generate accuracy graph
createAccuracyGraph     Generate accuracy graph
createStudy2GDS1KG      Create the Profile GDS file(s) for one or
                        multiple specific profiles using the
                        information from a RDS Sample description file
                        and the 1KG GDS file
demoKnownSuperPop1KG    The known super population ancestry of the demo
                        1KG reference profiles.
demoPCA1KG              The PCA results of the demo 1KG reference
                        dataset for demonstration purpose. Beware that
                        the PCA has been run on a very small subset of
                        the 1KG reference dataset and should not be
                        used to call ancestry inference on a real
                        profile.
demoPCASyntheticProfiles
                        The PCA result of demo synthetic profiles
                        projected on the demo subset 1KG reference PCA.
demoPedigreeEx1         The pedigree information about a demo profile
                        called 'ex1'.
estimateAllelicFraction
                        Estimate the allelic fraction of the pruned
                        SNVs for a specific profile
generateGDS1KG          Generate the GDS file that will contain the
                        information from Reference data set (reference
                        data set)
generateMapSnvSel       Generate the filter SNP information file in RDS
                        format
generatePhase1KG2GDS    Adding the phase information into the Reference
                        GDS file
generatePhaseRef        Adding the phase information into the Reference
                        GDS file
getRef1KGPop            Extract the specified column from the 1KG GDS
                        'sample.ref' node for the reference profiles
                        (real ancestry assignation)
getRefSuperPop          Extract the from the 1KG GDS 'sample.ref' node
                        for the reference profiles (real ancestry
                        assignation)
groupChr1KGSNV          Merge the genotyping files per chromosome into
                        one file
identifyRelative        Identify genetically unrelated patients in GDS
                        Reference file
identifyRelativeRef     Identify genetically unrelated patients in GDS
                        Reference file
inferAncestry           Run most steps leading to the ancestry
                        inference call on a specific DNA profile
inferAncestryDNA        Run most steps leading to the ancestry
                        inference call on a specific DNA profile (alias
                        for inferAncestry )
inferAncestryGeneAware
                        Run most steps leading to the ancestry
                        inference call on a specific RNA profile
matKNNSynthetic         A small 'data.frame' containing the inferred
                        ancestry on the synthetic profiles.
pedSynthetic            A small 'data.frame' containing the information
                        related to synthetic profiles. The ancestry of
                        the profiles used to generate the synthetic
                        profiles must be present.
prepPed1KG              Prepare the pedigree file using pedigree
                        information from Reference
prepSynthetic           Add information related to the synthetic
                        profiles (study and synthetic reference
                        profiles information) into a Profile GDS file
pruningSample           Compute the list of pruned SNVs for a specific
                        profile using the information from the
                        Reference GDS file and a linkage disequilibrium
                        analysis
runExomeAncestry        Run most steps leading to the ancestry
                        inference call on a specific exome profile
runRNAAncestry          Run most steps leading to the ancestry
                        inference call on a specific RNA profile
select1KGPop            Random selection of a specific number of
                        reference profiles in each subcontinental
                        population present in the 1KG GDS file
select1KGPopForSynthetic
                        Random selection of a specific number of
                        reference profiles in each subcontinental
                        population present in the 1KG GDS file ( same
                        as select1KGPop but the function doesn't need
                        gds object as parameters but the file name of
                        the referenceGDS )
snpPositionDemo         A small 'data.frame' containing the SNV
                        information.
snvListVCF              Generate a VCF with the information from the
                        SNPs that pass a cut-off threshold
splitSelectByPop        Group samples per subcontinental population
syntheticGeno           Generate synthetic profiles for each cancer
                        profile and 1KG reference profile combination
                        and add them to the Profile GDS file
