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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102 Calls: as.matrix -> as.matrix.Matrix -> as -> asMethod #385

Open ekinsnmz opened 1 year ago

ekinsnmz commented 1 year ago

Hi, I am trying to perform scenic. When I try to run exprMat <- as.matrix(seurat@assays$RNA@data) I receive the error.

library(tidyverse) library(Seurat) library(SCENIC) library(AUCell) library(RcisTarget) library(ComplexHeatmap)

options(error = function() traceback(2))

seurat<- readRDS("/shared/ifbstor1/projects/disease_gnr_pm/GSE184950/merged_filtered_umap_seurat_harmony_UMAP.rds")

seurat meta.data <- seurat@meta.data

DimPlot(seurat)

clusters <- c(pericyte = 31, pericyte =22, endothelial=23, endothelial=27, endothelial=39, endothelial=45, endothelial=9, opc= 12, opc=26, opc=38, opc=43, opc=46, opc=11, opc=32, oligodentrocyte= 3, oligodentrocyte= 4, oligodentrocyte= 5, oligodentrocyte= 52, oligodentrocyte= 29, oligodentrocyte= 13, oligodentrocyte= 40,oligodentrocyte= 1,oligodentrocyte= 48, oligodentrocyte= 51,oligodentrocyte= 10,oligodentrocyte= 2,oligodentrocyte= 37, oligodentrocyte= 8, oligodentrocyte= 25, oligodentrocyte= 0, microglia= 15, microglia= 35, microglia= 16, microglia= 20, microglia= 19, astrocyte= 18, astrocyte= 21, astrocyte= 24, astrocyte= 44, astrocyte= 17, astrocyte= 6, neuron= 36, neuron= 34, neuron=28, neuron=7,neuron=50, neuron=30, neuron=47, neuron=49, neuron=14, fibroblast=41, fibroblast=33, tcell= 42)

seurat$celltype <- names(clusters[match(seurat$seurat_clusters, clusters)])

DimPlot(seurat, group.by = "celltype")

exprMat <- as.matrix(seurat@assays$RNA@data)

Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102 Calls: as.matrix -> as.matrix.Matrix -> as -> asMethod

Any suggestion?