Description Usage Arguments Value Examples

View source: R/compare_omega.R

This function computes a re-ordering of the clusters from GoM model fit in one model to make it comparable with that from another. The two models are applied on the same set of samples with same number of clusters, but the features may change from one model to another. The two models may not be of same type as well. One could be a DAPC model, the other a standard topic model. Aids in checking for consistency in topic proportion patterns across multiple GoM methods or across different types of feature sets.

1 | ```
compare_omega(omega1, omega2)
``` |

`omega1` |
cluster membership proportion matrix (N x K) from model 1 |

`omega2` |
cluster membership proportion matrix (N x K) from model 2 |

Returns a list containing

`kl.dist` |
A symmetric KL divergence matrix across the re-ordered clusters of two omega matrices |

`kl.order_model2_topics` |
re-ordering of the clusters for omega2 to match the clusters for omega1 based on KL divergence |

`kl.information_content` |
A measure based on KL information to record how much information in omega2 is explained by omega1. Varies from 0 to 1 |

`cor.dist` |
A correlation matrix across the re-ordered clusters of two omega matrices |

`cor.order_model2_topics` |
re-ordering of the clusters for omega2 to match the clusters for omega1 based on correlation information |

`cor.information_content` |
A measure based on correlation information to record how much information in omega2 is explained by omega1. Varies from 0 to 1 |

1 2 3 4 5 6 7 8 | ```
tt=10;
omega1=matrix(rbind(gtools::rdirichlet(tt*10,c(3,4,2,6)),
gtools::rdirichlet(tt*10,c(1,4,6,3)),
gtools::rdirichlet(tt*10,c(4,1,2,2))), nrow=3*10*tt);
omega2=matrix(rbind(gtools::rdirichlet(tt*10,c(1,2,4,6)),
gtools::rdirichlet(tt*10,c(1,4,6,3)),
gtools::rdirichlet(tt*10,c(3,1,5,2))), nrow=3*10*tt);
out <- compare_omega(omega1, omega2)
``` |

Bioconductor-mirror/CountClust documentation built on May 29, 2017, 2:15 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.