| calcGRM | Function to calculate genomic relationship matrix (GRM) |
| CalcThreshold | Function to calculate threshold for GWAS |
| cumsumPos | Function to calculate cumulative position (beyond chromosome) |
| design.Z | Function to generate design matrix (Z) |
| EM3.cpp | Equation of mixed model for multi-kernel (slow, general... |
| EM3.linker.cpp | Equation of mixed model for multi-kernel (fast, for limited... |
| EMM1.cpp | Equation of mixed model for one kernel, GEMMA-based method... |
| EMM2.cpp | Equation of mixed model for one kernel, EMMA-based method... |
| EMM.cpp | Equation of mixed model for one kernel, a wrapper of two... |
| 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 |
| MAF.cut | Function to remove the minor alleles |
| make.full | Change a matrix to full-rank matrix |
| manhattan | Draw manhattan plot |
| manhattan2 | Draw manhattan plot (another method) |
| manhattan3 | Draw the effects of epistasis (3d plot and 2d plot) |
| manhattan.plus | Add points of -log10(p) corrected by kernel methods to... |
| modify.data | Function to modify genotype and phenotype data to match |
| plotHaploNetwork | Function to plot haplotype network from the estimated results |
| plotPhyloTree | Function to plot phylogenetic tree from the estimated results |
| qq | Draw qq plot |
| RAINBOW | RAINBOW: Perform Genome-Wide Asscoiation Study (GWAS) By... |
| RGWAS.epistasis | Check epistatic effects by kernel-based GWAS (genome-wide... |
| RGWAS.menu | Print the R code which you should perform for RAINBOW 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,... |
| RGWAS.twostep.epi | Perform normal GWAS (genome-wide association studies) first,... |
| Rice_geno_map | Physical map of rice genome |
| Rice_geno_score | Marker genotype 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.score | Calculate -log10(p) of epistatic effects with score test |
| 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... |
| 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... |
| 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... |
| welcome_to_RGWAS | Function to greet to users |
