RAINBOWR0.1.38 package

Function to adjust genomic relationship matrix (GRM) with subpopulatio...

Function to calculate genomic relationship matrix (GRM)

Function to calculate threshold for GWAS

Function to convert haplotype block list from PLINK to RAINBOWR format

Function to calculate cumulative position (beyond chromosome)

Function to generate design matrix (Z)

Equation of mixed model for multi-kernel considering covariance struct...

Equation of mixed model for multi-kernel (slow, general version)

Equation of mixed model for multi-kernel including using other package...

Equation of mixed model for multi-kernel (fast, for limited cases)

Equation of mixed model for multi-kernel using other packages (much fa...

Equation of mixed model for one kernel, a wrapper of two methods

Equation of mixed model for one kernel, GEMMA-based method (inplemente...

Equation of mixed model for one kernel, EMMA-based method (inplemented...

Function to estimate & plot haplotype network

Function to estimate & plot phylogenetic tree

Function to generate map for gene set

Generate pseudo phenotypic values

Function to judge the square matrix whether it is diagonal matrix or n...

Function to remove the minor alleles

Change a matrix to full-rank matrix

Add points of -log10(p) corrected by kernel methods to manhattan plot

Draw manhattan plot

Draw manhattan plot (another method)

Draw the effects of epistasis (3d plot and 2d plot)

Function to modify genotype and phenotype data to match

Function to parallelize computation with various methods

Function to plot haplotype network from the estimated results

Function to plot phylogenetic tree from the estimated results

Draw qq plot

RAINBOWR: Perform Genome-Wide Asscoiation Study (GWAS) By Kernel-Based...

Check epistatic effects by kernel-based GWAS (genome-wide association ...

Print the R code which you should perform for RAINBOWR GWAS

Testing multiple SNPs and their interaction with some kernel simultane...

Testing multiple SNPs simultaneously for GWAS

Perform normal GWAS including interaction (test each single SNP)

Perform normal GWAS (test each single SNP)

Perform normal GWAS (genome-wide association studies) first, then chec...

Perform normal GWAS (genome-wide association studies) first, then perf...

Physical map of rice genome

Marker genotype of rice genome

Physical map of rice genome

Phenotype data of rice field trial

Calculate -log10(p) of epistatic effects by LR test (multi-cores)

Calculate -log10(p) of epistatic effects by LR test

Calculate -log10(p) of epistatic effects with score test (multi-cores)

Calculate -log10(p) of epistatic effects with score test

Calculate -log10(p) for single-SNP GWAS with interaction (multi-cores)

Calculate -log10(p) for single-SNP GWAS with interaction

Calculate -log10(p) of each SNP-set and its interaction with kernels b...

Calculate -log10(p) of each SNP-set and its interaction with kernels b...

Calculate -log10(p) of each SNP-set by the LR test (multi-cores)

Calculate -log10(p) of each SNP-set by the LR test

Calculate -log10(p) for single-SNP GWAS (multi-cores)

Calculate -log10(p) for single-SNP GWAS

Calculate -log10(p) of each SNP-set by the score test (multi-cores)

Calculate -log10(p) of each SNP-set by the score test

Calculte -log10(p) by score test (slow, for general cases)

Calculte -log10(p) by score test (fast, for limited cases)

Function to view the first part of data (like head(), tail())

Perform spectral decomposition (inplemented by Rcpp)

Calculate some summary statistics of GWAS (genome-wide association stu...

Function to greet to users