Description Usage Arguments Value Author(s)

Enrichment analysis and hypothesis testing by comparing t-statistics from a given gene set to genome-wide t-statistics. Evaluated with pinnacle linear mixed model with either local or global correlation structure.

Gene set enrichment analysis based on genomic intervals from ChIP-seq, ATAC-seq, etc.

1 2 3 |

`vobj` |
voom object |

`fit` |
model fit from lmFit() in limma or dream() in variancePartition |

`L` |
contrast matrix |

`corrStruct` |
object from evalCorrelationDecomp() storing SVD of covariance matrix |

`geneSets` |
list of genesets |

`target` |
GRanges object of locations of genes |

`rank` |
of decomposition to bet set by truncating trailing eigen values |

`varianceFraction` |
fraction of variance to retain after truncating trailing eigen values |

`decay` |
weight function parameter |

`squaredCorr` |
Compute decomposition of squared correlation for two-sided test |

`quiet` |
suppress messages |

table of enrichment statistics

Gabriel E. Hoffman

GabrielHoffman/pinnacle documentation built on May 3, 2019, 3:02 p.m.

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.