| RAINBOWR-package | RAINBOWR: Perform Genome-Wide Asscoiation Study (GWAS) By Kernel-Based Methods | 
| adjustGRM | Function to adjust genomic relationship matrix (GRM) with subpopulations | 
| calcGRM | Function to calculate genomic relationship matrix (GRM) | 
| CalcThreshold | Function to calculate threshold for GWAS | 
| 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) | 
| 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) | 
| 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 | 
| MAF.cut | Function to remove the minor alleles | 
| 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 | 
| 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_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 | 
| Rice_Zhao_etal | Rice_Zhao_etal: | 
| score.calc | Calculate -log10(p) for single-SNP GWAS | 
| 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.LR | Calculate -log10(p) of each SNP-set by the LR test | 
| 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.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.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) | 
| See | Function to view the first part of data (like head(), tail()) | 
| spectralG.cpp | Perform spectral decomposition (inplemented by Rcpp) | 
| SS_gwas | Calculate some summary statistics of GWAS (genome-wide association studies) for simulation study | 
| welcome_to_RGWAS | Function to greet to users |