suggest_best_k-ConsensusPartition-method {cola} | R Documentation |
Suggest the best number of partitions
## S4 method for signature 'ConsensusPartition' suggest_best_k(object, jaccard_index_cutoff = 0.95)
object |
A |
jaccard_index_cutoff |
The cutoff for Jaccard index compared to previous k. |
The best k is selected according to following rules:
All k with Jaccard index larger than 0.95 are removed because increasing k does not provide enough extra information. If all k are removed, it is marked as no subgroup is detected.
For all k with 1-PAC score larger than 0.9, the maximal k is taken as the best k, and other k are marked as optional k.
If it does not fit the second rule. The k with the maximal vote of the highest 1-PAC score, highest mean silhouette, and highest concordance is taken as the best k.
Additionally, if 1-PAC for the best k is larger than 0.9 (10 the partition), cola marks it as a stable partition. It should be noted that it is difficult to find the best k deterministically, we encourage users to compare results for all k and determine a proper one which best explain their studies.
The best k.
Zuguang Gu <z.gu@dkfz.de>
data(cola_rl) obj = cola_rl["sd", "kmeans"] suggest_best_k(obj)