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hi team, I try to build a ts file by
ts <- tSpace(df = your_data, K = 20, L = 15, D = 'pearson_correlation', graph = 5, trajectories = 200, wp = 15, dr = 'pca', core_no = 2)
However, how to create the "your_data" from a seurat object? I try the following two ways:
- data.table<- as.matrix(GetAssayData(seurat_object, slot = "data"))
ts <- tSpace(df = data.table,
-
K = 20, L = 15, -
D = 'pearson_correlation', -
graph = 5, -
trajectories = 200, -
wp = 15, dr = 'pca', core_no = 8)
Step 1:Finding graphError in graph.adjacency.sparse(adjmatrix, mode = mode, weighted = weighted, :
not a square matrix
- data.table<- as.matrix(GetAssayData(seurat_object, slot = "data"))
data.table <- as(data.table, 'sparseMatrix')
ts <- tSpace(df = data.table,
-
K = 20, L = 15, -
D = 'pearson_correlation', -
graph = 5, -
trajectories = 200, -
wp = 15, dr = 'pca', core_no = 8)
Step 1:Finding graphError in { :
task 1 failed - "unable to find an inherited method for function ‘[’ for signature ‘"dgCMatrix"’"
How to create an eligible "your_data" file? Thanks a lot!
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