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OscarGVelasco / ClusterFoldSimilarity

Calculate cluster similarity between clusters from different single cell datasets/batches/samples.
MIT License
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Error in lapply #4

Closed josemss closed 5 months ago

josemss commented 1 year ago

Hi Oscar, I'm Jose.

When I run lapply to normalise, scale, etc. my seurat objects I get an error. Code: singlecell.object.list <- lapply(X = singlecell.object.list, FUN = function(x){ x <- NormalizeData(x) x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 1000) x <- ScaleData(x,features = VariableFeatures(x)) x <- RunPCA(x, features = VariableFeatures(object = x)) x <- FindNeighbors(x, dims = seq(10)) x <- FindClusters(x, resolution = 0.1) }) Error: Computing nearest neighbor graph Computing SNN Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate' not found

Attached is my script. Thanks. ClusterFoldSimilarity_GEO_datasets.txt

OscarGVelasco commented 5 months ago

The whole algorithm has been changed with a new similarity metric formula and approach.