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holab-hku / DCATS

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knn_simMat Error #16

Closed gianfilippo closed 1 month ago

gianfilippo commented 1 month ago

Hi, when I run knn_simMat on my Seurat object knn_mat = knn_simMat(scdata@graphs$SNN,scdata$singleR) I get the following error Error in KNN_matrix[idx_i, ][, idx_j] : incorrect number of dimensions

My scdata object is scdata An object of class Seurat 35285 features across 73877 samples within 2 assays Active assay: RNA (32285 features, 0 variable features) 1 other assay present: integrated 3 dimensional reductions calculated: pca, umap, tsne

my scdata@graphs$SNN dim(scdata@graphs$SNN) [1] 73877 73877

What am I doing wrong ?

Thanks

linxy29 commented 1 month ago

Hi @gianfilippo , This problem might be caused by the scdata$singleR. Could you check 1) the dimension of scdata$singleR through length(scdata$singleR); and the number of cell types that exist through unique(scdata$singleR)?

gianfilippo commented 1 month ago

Hi, thanks. Not sure what happened. I tried with the full dataset and it worked. Best