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.
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