Error in getMatrixFromProject

[tianchen2019]

Describe the bug

when i run getMatrixFromProject(proj,useMatrix = "GeneScoreMatrix").The error message is as follows: ArchR logging to : ArchRLogs/ArchR-getMatrixFromProject-44db558acd0bf-Date-2021-03-25_Time-11-51-02.log If there is an issue, please report to github with logFile! 2021-03-25 11:54:52 : Organizing colData, 3.834 mins elapsed. 2021-03-25 11:54:55 : Organizing rowData, 3.888 mins elapsed. 2021-03-25 11:54:55 : Organizing rowRanges, 3.889 mins elapsed. 2021-03-25 11:54:55 : Organizing Assays (1 of 1), 3.889 mins elapsed. Error in .cbind2Csp(x, y) : Cholmod error 'problem too large' at file ../Core/cholmod_sparse.c, line 92. The reason might be that the matrix is too big. the number of cell is 380000.

[rcorces]

As indicated in the issue template, please attach your log file.

also, this is a similar error to https://github.com/GreenleafLab/ArchR/issues/547

[jgranja24]

Hi @tianchen2019, you cant load this matrix into R because its way too large and the gene score matrix is less sparse than desired. What are you trying to do with this matrix? I would import the matrix from each sample and save them individually as processed files if that is what you desire?

[tianchen2019]

Hi @tianchen2019, you cant load this matrix into R because its way too large and the gene score matrix is less sparse than desired. What are you trying to do with this matrix? I would import the matrix from each sample and save them individually as processed files if that is what you desire?

I plan to export the matrix and use imputeMatrix to get the imputation matrix. Use this matrix to calculate the "expression score" of the gene set to help me define the cell type.

[jgranja24]

Hmmm what do you mean by '"expression score" of the gene set' have you seen our module score function? See https://github.com/GreenleafLab/ArchR/issues/308.

[rcorces]

Closing due to inactivity. Feel free to comment again here if you still need help.

[A-legac45]

Hello, I have a multiomic data and I would like to incorporate in my seurat object the genescorematrix from archr

The following step work but I am troubeling by adding it to the seurat object I am losing the genes names and I am not able to do featureplot at the end

Extraire la GeneScoreMatrix

geneScoreMatrix <- getMatrixFromProject(ArchRProj = project_Peaks_RES0.9_subcluster, useMatrix = "GeneScoreMatrix")

genes names

geneScoreMatrix@elementMetadata$name

Convertir en dgCMatrix

geneScoreMatrix_dgc <- as(geneScoreMatrix@assays@data$GeneScoreMatrix, "dgCMatrix")