single cell ATAC-seq cicero gene activities matrix in Seurat

[Elham Jafari]

Hi everyone!

I am loading my single-cell ATACseq data using cicero, and then I create gene activity scores according to the tutorial. My goal is to use this cicero gene activity score object in Seurat. Based on Seurat, I can use cicero object in their pipeline as they mentioned that "Seurat's method is compatible with any method that returns a gene by cell-matrix (e.g. Cicero)"

My problem is that I have tried this cicero object as an input for several functions of Seurat's tutorial, but it gives me errors all the time. (I tried it in CreateGeneActivityMatrix(), CreateSeuratObject(), and etc.) For example when I run the following:

activity.matrix <- CreateGeneActivityMatrix(peak.matrix = cicero_gene_activities, annotation.file ="data/Homo_sapiens.GRCh38.100.gtf", seq.levels = c(1:22, "X", "Y"), upstream = 2000, verbose = TRUE) 

 Error in .get_data_frame_col_as_numeric(df, granges_cols[["start"]]) : some values in the "start" column cannot be turned into numeric values

Then, I ignored the first few functions that throw an error and tried going through the rest of the tutorial, but then I faced an error here:

pbmc.atac <- RunLSI(pbmc.atac, n = 50, scale.max = NULL) 

 Error in as(object = data, Class = "dgCMatrix") : no method or default for coercing "numeric" to "dgCMatrix"

I am very new to Seurat so I couldn't figure the errors out by searching. I would appreciate any comments on how to proceed forward with Seurat using my cicero object.

Thanks in advance!

[hpl...@gmail.com]

Hello,

I suspect that you'll need to ask this of the Seurat developers as these are Seurat functions - my only guess: check that your cicero_gene_activites object is in fact a valid matrix (just using head(cicero_gene_activities) for example).

If any users have ported to Seurat, it'd be helpful to hear too!

Best,

Hannah