CalcThreshold           Function to calculate threshold for GWAS
EM3.cpp                 Equation of mixed model for multi-kernel (slow,
                        general version)
EM3.linker.cpp          Equation of mixed model for multi-kernel (fast,
                        for limited cases)
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.normal            Perform normal GWAS (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_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())
calcGRM                 Function to calculate genomic relationship
                        matrix (GRM)
cumsumPos               Function to calculate cumulative position
                        (beyond chromosome)
design.Z                Function to generate design matrix (Z)
estPhylo                Function to estimate & plot phylogenetic tree
genesetmap              Function to generate map for gene set
genetrait               Generate pseudo phenotypic values
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
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.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.score
                        Calculate -log10(p) of epistatic effects with
                        score test
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
