Computes gene prioritisation scores based on promoter capture Hi-C data

approx.bf.p | This function computes posterior probabilities for a variant... |

compute_cogs | This function computes COGS scores for a given trait across a... |

csnps.gr | csnps.gr Coding SNPs for chromosome 22. |

digest.gr | digest.gr HindIII restriction digest for chromosome 22. |

feature.sets | feature.sets Feature sets from Javierre et al pcHi-C dataset... |

fix_chr | This function fixes chromosomes so they are numeric |

ld.gr | ld.gr HapMap approx 1cM LD blocks for chromosome 22. |

load_capture_design | This loads a capture design file with columns fragid and... |

load_digest | This loads a restriction digest file with columns... |

load_gwas | This function loads and checks set of univariate P values for... |

load_ld_regions | This function checks and loads and checks a set of non... |

load_ref_maf | This function checks and loads a reference set of maf expects... |

logsum | helper function to sum logs without loss of precision... |

maf.DT | maf.DT Reference minor allele frequencies from UK10K for... |

make_csnps | This function loads in a coding SNPs matched to a given... |

make_pchic | This function computes loads in a set of promoter capture... |

make_vprom | This function computes 'Virtual' promoter regions. These are... |

t1d.DT | t1d.DT GWAS data from Cooper et al. for Type 1 diabetes for... |

Var.data | helper function to compute shrinkage factor for a... |

Var.data.cc | helper function to compute shrinkage factor for a... |

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