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Core-Bioinformatics / ClustAssess

Tools for assessing clustering robustness
https://core-bioinformatics.github.io/ClustAssess/
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about the tools #3

Open Bao110110 opened 8 months ago

Bao110110 commented 8 months ago

excuse me, when first using this tools , i get a question:

cc_res = consensus_cluster(your_data, n_reps=50, k_max=20, p_sample=0.8, p_feature=0.8)

here, what type is the "your_data"? could it be a Seurat object ? when i try it with a seurat object, i face an error:

> cc_res = consensus_cluster(agecell, n_reps=50, k_max=20, p_sample=0.8, p_feature=0.8)
Calculating consensus clustering
Error in as.vector(data) : 
  no method for coercing this S4 class to a vector

hoping a help ，thank you

AndiMunteanu commented 1 month ago

Hello and sorry for reaching out this late!

We have updated the package's website. Here you have an example that shows you how to use the Seurat's object to get the right input for the consensus_clustering function. your_data should be a samples x features normalized data matrix.

Hopefully that answers the question.

Andi