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KlugerLab / ALRA

Imputation method for scRNA-seq based on low-rank approximation
MIT License
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GetAssayData(pbmc, slot = "counts") gives 0 x 0 matrix #14

Open Lumskie opened 2 years ago

Lumskie commented 2 years ago

Hi,

I have been doing impuation with ALRA for past few days and results seems really promising for my data s it keeps the biological variation intact. However, I need to supply this data into SCENIC to find the active Transcription factors. For this I need the exprMat of the data. I usually derive it using the following code;

exprMat<-GetAssayData(seurat, slot = "counts") exprMat<-as.matrix(exprMat)

However, this is giving me 0 x0 matrix. How can I get the exprMat from alra data? @JunZhao1990 @linqiaozhi

Thank you in advance

JunZhao1990 commented 2 years ago

Hi @Lumskie, ALRA result will be saved in the data slot, rather than counts slot. Could you try exprMat<-GetAssayData(seurat, slot = "data")?