Bcov_discovery          Covariate data file of the discovery dataset
                        when the outcome is binary. This contains
                        covariate information of the individuals in the
                        discovery dataset following confounders.
Bcov_target             Covariate data file of the target dataset when
                        the outcome is binary. This contains covariate
                        information of the individuals in the target
                        dataset following confounders.
Bphe_discovery          Phenotype data file of the discovery dataset
                        when the outcome is binary. This contains
                        phenotype information of the individuals in the
                        discovery dataset.
Bphe_target             Phenotype data file of the target dataset when
                        the outcome is binary. This contains phenotype
                        information of the individuals in the target
                        dataset.
DummyData.bim           PLINK .bim file
DummyData.fam           PLINK .fam file
DummyData.map           PLINK .map file
DummyData.ped           PLINK .ped file
GWAS_binary             GWAS_binary function This function performs
                        GWAS using plink2 and outputs the GWAS summary
                        statistics with additive SNP effects. Users may
                        save the output in a user-specified file (see
                        example).
GWAS_quantitative       GWAS_quantitative function This function
                        performs GWAS using plink2 and outputs the GWAS
                        summary statistics with additive SNP effects.
                        Users may save the output in a user-specified
                        file (see example).
GWEIS_binary            GWEIS_binary function This function performs
                        GWEIS using plink2 and outputs the GWEIS
                        summary statistics with additive SNP effects
                        and interaction SNP effects. Users may save the
                        outputs in separate user-specified files (see
                        examples).
GWEIS_quantitative      GWEIS_quantitative function This function
                        performs GWEIS using plink2 and outputs the
                        GWEIS summary statistics with additive SNP
                        effects and interaction SNP effects separately.
                        It is recommended to save the outputs in
                        separate user-specified files (see examples).
PRS_binary              PRS_binary function This function uses plink2
                        and outputs Polygenic Risk Scores (PRSs) of all
                        the individuals, using pre-generated GWAS
                        and/or GWEIS summary statistics. Note that the
                        input used in this function can be generated by
                        using GWAS_binary and/or GWEIS_binary
                        functions. Users may save the output in a
                        user-specified file (see examples).
PRS_quantitative        PRS_quantitative function This function uses
                        plink2 and outputs Polygenic Risk Scores (PRSs)
                        of all the individuals, using pre-generated
                        GWAS and/or GWEIS summary statistics. Note that
                        the input used in this function can be
                        generated by using GWAS_quantitative and/or
                        GWEIS_quantitative functions. Users may save
                        the output in a user-specified file (see
                        examples).
Qcov_discovery          Covariate data file of the discovery dataset
                        when the outcome is quantitative. This contains
                        covariate information of the individuals in the
                        discovery dataset following confounders.
Qcov_target             Covariate data file of the target dataset when
                        the outcome is quantitative. This contains
                        covariate information of the individuals in the
                        target dataset following confounders.
Qphe_discovery          Phenotype data file of the discovery dataset
                        when the outcome is quantitative. This contains
                        phenotype information of the individuals in the
                        discovery dataset.
Qphe_target             Phenotype data file of the target dataset when
                        the outcome is quantitative. This contains
                        phenotype information of the individuals in the
                        target dataset.
summary_permuted_binary
                        summary_permuted_binary function This function
                        outputs the p value of permuted model in the
                        target dataset, using pre-generated Polygenic
                        Risk Scores (PRSs) of all the individuals. Note
                        that the input used in this function can be
                        generated by using PRS_quantitative function.
                        It is recommended to run this function, if you
                        choose to fit 'PRS_gxe x E' interaction
                        component (i.e. novel proposed model, Model 5)
                        when generating risk scores. If the 'PRS_gxe x
                        E' term is significant in Model 5, and
                        insignificant in Model 5* (permuted p value),
                        consider that the 'PRS_gxe x E' interaction
                        component is actually insignificant (always
                        give priority to the p value obtained from the
                        permuted model).
summary_permuted_quantitative
                        summary_permuted_quantitative function This
                        function outputs the p value of permuted model
                        in the target dataset, using pre-generated
                        Polygenic Risk Scores (PRSs) of all the
                        individuals. Note that the input used in this
                        function can be generated by using
                        PRS_quantitative functions. It is recommended
                        to run this function, if you choose to fit
                        'PRS_gxe x E' interaction component (i.e. novel
                        proposed model, Model 4) when generating risk
                        scores. If the 'PRS_gxe x E' term is
                        significant in Model 4, and insignificant in
                        Model 4* (permuted p value), consider that the
                        'PRS_gxe x E' interaction component is actually
                        insignificant (always give priority to the p
                        value obtained from the permuted model).
summary_regular_binary
                        summary_regular_binary function This function
                        outputs the summary of regular model and final
                        risk score values of each individual in the
                        target dataset using pre-generated Polygenic
                        Risk Scores (PRSs) of all the individuals. Note
                        that the input used in this function can be
                        generated by using PRS_binary function.
summary_regular_quantitative
                        summary_regular_quantitative function This
                        function outputs the summary of regular model
                        and final risk score values of each individual
                        in the target dataset using pre-generated
                        Polygenic Risk Scores (PRSs) of all the
                        individuals. Note that the input used in this
                        function can be generated by using
                        PRS_quantitative function.
