Genome-Wide Association Study with SNP-Set Methods

Vignettes

143

32

63

**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**qq:**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...**Browse all...**

View source: R/functions_for_RGWAS.R

R Documentation |

Draw qq plot

```
qq(scores)
```

`scores` |
A vector of -log10(p) for each marker |

Draw qq plot

What can we improve?

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close