Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

AGT | AGT data set |

as.bed.matrix | Creation of a bed.matrix |

association.test | Association Test |

bed.loadings | SNP loadings |

bed.matrix-class | Class '"bed.matrix"' |

DM | Dominance Matrix |

dupli | Small data set to illustrate 'SNP.rm.duplicates' |

gaston-package | gaston |

GRM | Genetic Relationship Matrix |

is.autosome | Autosomes and X, Y, MT chromosomes |

LCT | LCT data set |

LD | Linkage Disequilibrium |

LD.plot | Plot Linkage Disequilibrium |

LD.thin | LD thinning |

lik.contour | Contour plot for two parameters likelihood |

lmm.aireml | Linear mixed model fitting with AIREML |

lmm.diago | Linear mixed model fitting with the diagonalization trick |

lmm.diago.likelihood | Likelihood of a linear mixed model |

lmm.restricted.likelihood | Likelihood of a linear mixed model |

lmm.simu | Linear mixed model data simulation |

logistic.mm.aireml | Logistic mixed model fitting with Penalized Quasi-Likelihood... |

manhattan | Manhattan plot |

qqplot.pvalues | QQ plot of p-values |

random.pm | Random square definite positive matrix |

read.bed.matrix | Read a 'bed.matrix' |

read.vcf | Create a 'bed.matrix' from VCF files |

reshape.GRM | Reshape a Genetic Relationship Matrix |

score.fixed | Score Test for Covariates with Fixed Effects in Linear or... |

score.variance | Variance Component Test in Linear or Logistic Mixed Model |

select.inds | Subsetting from a 'bed.matrix' |

select.snps | Subsetting from a 'bed.matrix' |

set.dist | Set Genetic Distance |

set.genomic.sex | Genomic Sex |

set.hwe | Hardy-Weinberg Equilibrium |

set.stats | Basic statistics for a 'bed.matrix' |

SNP.duplicated | Duplicated SNPs |

SNP.match | SNP matching |

SNP.rm.duplicates | Remove duplicated SNPs |

Tests | Evaluation of a condition on SNPS or individuals in a... |

TTN | TTN data set |

write.bed.matrix | Save a 'bed.matrix' |

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