Affinity test for identifying regulatory SNPs

atSNP-package | atSNP: affinity tests for regulatory SNP detection |

ComputeMotifScore | Compute the scores for SNP effects on motifs. |

ComputePValues | Compute p-values for affinity scores. |

dtMotifMatch | Compute the augmented matching subsequence on SNP and... |

encode_motif | A motif library containing 2065 motifs downloaded from... |

encode_motifinfo | The information for the motif library downloaded from... |

GetIUPACSequence | Get the IUPAC sequence of a motif. |

jaspar_motif | A motif library containing 593 motifs downloaded from... |

jaspar_motifinfo | The information for the motif library downloaded from... |

LoadFastaData | Load the SNP data from fasta files. |

LoadMotifLibrary | Load position weight matrices. |

LoadSNPData | Load the SNP information and code the genome sequences around... |

MatchSubsequence | Compute the matching subsequence. |

motif_library | A sample motif library. |

motif_match | Composit logo plotting input containing motif scores, the... |

motif_scores | Scores for the sample snp data computed based on the motif... |

plotMotifMatch | Plot sequence logos of the position weight matrix of the... |

prior | Default stationary distribution for nucleotide sequences in... |

snpInfo | A data set for SNP information. |

snp_tbl | A data frame for SNP information. |

transition | Default transition probability matrix for nucleotide... |

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