Description Usage Arguments Value Author(s)

Creates a distance matrix for pwms

1 2 3 4 5 | ```
pwmsDistanceMatrix(pwms, diagonal_value = 0, bottom_default_value = NULL,
divergence = shannonDivergence,
unaligned_penalty = divergencePenaltyForUnaligned,
try_reverse_complement = TRUE, base_distribution = NULL,
length_normalization = FALSE)
``` |

`pwms` |
list of pwms |

`diagonal_value` |
value to put on diagonal. |

`bottom_default_value` |
value to put on bottom triangle. Set to NULL to get symmetric distance matrix. |

`divergence` |
divergence measure. |

`unaligned_penalty` |
is a function for localPwmAlignment. |

`try_reverse_complement` |
if True, alignment will try reverse complement pwms |

`base_distribution` |
is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used |

`length_normalization` |
is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used |

list

Lando Andrey

DiffLogo documentation built on Nov. 1, 2018, 2:24 a.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.