Description Usage Arguments Value

A wrapper for dist function.

1 2 3 4 | ```
generic_dist(X, method = c("manhattan", "euclidean", "exp manhattan",
"exp euclidean", "maximum", "canberra", "binary", "minkowski",
"jaccard"), log_trans = TRUE, log_base = 10, min_row_sum = 100,
min_row_prevalence = 5)
``` |

`X` |
A data matrix, e.g. gene expression |

`method` |
a character string indicating which distance method to use. |

`log_trans` |
A boolean indicating whether to log transform the data prio to distance computation (log(X + 1)). Default is FALSE. |

`log_base` |
A number indicating base for log transformation. Default is 10. |

`min_row_sum` |
A scalar indicating the minimum feature (species) summ across columns (samples) to be kept for distance computation. Only used for Jaccard distance. |

`min_row_prevalence` |
An integer indicating the minimum prevalence (non-zero occurance) of a feature (species) across samples to be kept for distance computation. Only used for Jaccard distance. |

A dissimilarity matrix, D.

nlhuong/buds documentation built on May 17, 2019, 3:13 a.m.

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