slot used by a function of Seurat and optimal number of clusters #5152
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pengxin2019
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Hi Tim,
Can you give me some suggestions on how to find out the slot used by a function in Seurat? like
FindClustersOne of my plans is to get the data used by
FindClustersand then use this data to check what should be the optimal number of clusters by using Silhouette Method or Gap Statistic though I might would have to use different clustering method..Another plan is to access the integrated_lsi coordinates with Embeddings(object = object[["integrated_lsi"]]) and compute the centroids by averaging the coordinates for the cells in each cluster. Then the eclidean distance could be calculated between the clusters using that metric. this solution is mentioned here #1419
Do you think it would be a stable method to evaluate the optimal number of clusters since the sum of distance between clusters should be smallest with the optimal number of cluster?
Thanks
Best
Penny
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