SNPs-based whole genome association studies

association | Association analysis between a single SNP and a given... |

BonferroniSig | Bonferroni correction of p values |

dscore | Exact distribution of a genetic score |

GenomicControl | Population substructure |

getGeneSymbol | Get gene symbol from a list of SNPs |

getLocusInfo | Get info from snpStats objects to be passed to Locus Zoom |

getSignificantSNPs | Extract significant SNPs from an object of class... |

haplointeraction | Haplotype interaction with a covariate |

HapMap | SNPs from HapMap project |

inheritance | Collapsing (or recoding) genotypes into different categories... |

int | Identify interaction term |

interactionPval | Two-dimensional SNP analysis for association studies |

intervals | Print ORs and 95% confidence intervals for an object of class... |

isMonomorphic | Check whether a SNP is Monomorphic |

LD | max-statistic for a 2x3 table |

makegeno | Create a group of locus objects from some SNPs, assign to... |

maxstat | max-statistic for a 2x3 table |

odds | Extract odds ratios, 95% CI and pvalues |

permTest | Permutation test analysis |

plotMissing | Plot of missing genotypes |

plotWGassociation | Function to plot -log p values from an object of class... |

qqpval | Functions for inspecting population substructure |

related | Get related samples |

scanWGassociation | Whole genome association analysis |

setupSNP | Convert columns in a dataframe to class 'snp' |

snp | SNP object |

SNPassoc-internal | Internal SNPstat functions |

SNPs | SNPs in a case-control study |

sortSNPs | Sort a vector of SNPs by genomic position |

tableHWE | Test for Hardy-Weinberg Equilibrium |

Tablemeanse | Descriptive sample size, mean, and standard error |

TableNPer | Descriptive sample size and percentage |

WGassociation | Whole genome association analysis |

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