Genome-Wide Association Study with SNP-Set Methods

adjustGRM | Function to adjust genomic relationship matrix (GRM) with... |

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... |

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.general | Equation of mixed model for multi-kernel including using... |

EM3.linker.cpp | Equation of mixed model for multi-kernel (fast, for limited... |

EM3.op | Equation of mixed model for multi-kernel using other packages... |

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 |

is.diag | Function to judge the square matrix whether it is diagonal... |

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 |

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 |

Draw qq plot | |

RAINBOWR | RAINBOWR: 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 RAINBOWR GWAS |

RGWAS.multisnp | Testing multiple SNPs simultaneously for GWAS |

RGWAS.multisnp.interaction | Testing multiple SNPs and their interaction with some kernel... |

RGWAS.normal | Perform normal GWAS (test each single SNP) |

RGWAS.normal.interaction | Perform normal GWAS including interaction (test each single... |

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_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... |

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... |

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... |

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... |

score.calc.LR.int.MC | Calculate -log10(p) of each SNP-set and its interaction with... |

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 |

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