CalcThreshold           Function to calculate threshold for GWAS
EM3.cov                 Equation of mixed model for multi-kernel
                        considering covariance structure between
                        kernels
EM3.cpp                 Equation of mixed model for multi-kernel (slow,
                        general version)
EM3.general             Equation of mixed model for multi-kernel
                        including using other packages (with other
                        packages, much faster than EM3.cpp)
EM3.linker.cpp          Equation of mixed model for multi-kernel (fast,
                        for limited cases)
EM3.op                  Equation of mixed model for multi-kernel using
                        other packages (much faster than EM3.cpp)
EMM.cpp                 Equation of mixed model for one kernel, a
                        wrapper of two methods
EMM1.cpp                Equation of mixed model for one kernel,
                        GEMMA-based method (inplemented by Rcpp)
EMM2.cpp                Equation of mixed model for one kernel,
                        EMMA-based method (inplemented by Rcpp)
MAF.cut                 Function to remove the minor alleles
RAINBOWR                RAINBOWR: Perform Genome-Wide Asscoiation Study
                        (GWAS) By Kernel-Based Methods
RGWAS.epistasis         Check epistatic effects by kernel-based GWAS
                        (genome-wide association studies)
RGWAS.menu              Print the R code which you should perform for
                        RAINBOWR GWAS
RGWAS.multisnp          Testing multiple SNPs simultaneously for GWAS
RGWAS.multisnp.interaction
                        Testing multiple SNPs and their interaction
                        with some kernel simultaneously for GWAS
RGWAS.normal            Perform normal GWAS (test each single SNP)
RGWAS.normal.interaction
                        Perform normal GWAS including interaction (test
                        each single SNP)
RGWAS.twostep           Perform normal GWAS (genome-wide association
                        studies) first, then perform SNP-set GWAS for
                        relatively significant markers
RGWAS.twostep.epi       Perform normal GWAS (genome-wide association
                        studies) first, then check epistatic effects
                        for relatively significant markers
Rice_Zhao_etal          Rice_Zhao_etal:
Rice_geno_map           Physical map of rice genome
Rice_geno_score         Marker genotype of rice genome
Rice_haplo_block        Physical map of rice genome
Rice_pheno              Phenotype data of rice field trial
SS_gwas                 Calculate some summary statistics of GWAS
                        (genome-wide association studies) for
                        simulation study
See                     Function to view the first part of data (like
                        head(), tail())
adjustGRM               Function to adjust genomic relationship matrix
                        (GRM) with subpopulations
calcGRM                 Function to calculate genomic relationship
                        matrix (GRM)
convertBlockList        Function to convert haplotype block list from
                        PLINK to RAINBOWR format
cumsumPos               Function to calculate cumulative position
                        (beyond chromosome)
design.Z                Function to generate design matrix (Z)
estNetwork              Function to estimate & plot haplotype network
estPhylo                Function to estimate & plot phylogenetic tree
genesetmap              Function to generate map for gene set
genetrait               Generate pseudo phenotypic values
is.diag                 Function to judge the square matrix whether it
                        is diagonal matrix or not
make.full               Change a matrix to full-rank matrix
manhattan               Draw manhattan plot
manhattan.plus          Add points of -log10(p) corrected by kernel
                        methods to manhattan plot
manhattan2              Draw manhattan plot (another method)
manhattan3              Draw the effects of epistasis (3d plot and 2d
                        plot)
modify.data             Function to modify genotype and phenotype data
                        to match
parallel.compute        Function to parallelize computation with
                        various methods
plotHaploNetwork        Function to plot haplotype network from the
                        estimated results
plotPhyloTree           Function to plot phylogenetic tree from the
                        estimated results
qq                      Draw qq plot
score.calc              Calculate -log10(p) for single-SNP GWAS
score.calc.LR           Calculate -log10(p) of each SNP-set by the LR
                        test
score.calc.LR.MC        Calculate -log10(p) of each SNP-set by the LR
                        test (multi-cores)
score.calc.LR.int       Calculate -log10(p) of each SNP-set and its
                        interaction with kernels by the LR test
score.calc.LR.int.MC    Calculate -log10(p) of each SNP-set and its
                        interaction with kernels by the LR test
                        (multi-cores)
score.calc.MC           Calculate -log10(p) for single-SNP GWAS
                        (multi-cores)
score.calc.epistasis.LR
                        Calculate -log10(p) of epistatic effects by LR
                        test
score.calc.epistasis.LR.MC
                        Calculate -log10(p) of epistatic effects by LR
                        test (multi-cores)
score.calc.epistasis.score
                        Calculate -log10(p) of epistatic effects with
                        score test
score.calc.epistasis.score.MC
                        Calculate -log10(p) of epistatic effects with
                        score test (multi-cores)
score.calc.int          Calculate -log10(p) for single-SNP GWAS with
                        interaction
score.calc.int.MC       Calculate -log10(p) for single-SNP GWAS with
                        interaction (multi-cores)
score.calc.score        Calculate -log10(p) of each SNP-set by the
                        score test
score.calc.score.MC     Calculate -log10(p) of each SNP-set by the
                        score test (multi-cores)
score.cpp               Calculte -log10(p) by score test (slow, for
                        general cases)
score.linker.cpp        Calculte -log10(p) by score test (fast, for
                        limited cases)
spectralG.cpp           Perform spectral decomposition (inplemented by
                        Rcpp)
welcome_to_RGWAS        Function to greet to users
