Converting merged Seurat object back to dgCMatrix

Question

[LacquerHed]

Have a merged Seurat object as follows:

CtrlCombined <- merge(ctrl1, y = c(ctrl2, ctrl3), add.cell.ids = c("WT_151", "WT_152", "WT_156"), project = "Combined")
Ctrl <- CtrlCombined

Would like to convert the merged object back into a single dgCMatrix as imported by Read10X

Thanks.

[rpolicastro]

Read10X imports a market exchange matrix along with text files that contain the features and cell ids, not a dgCMatrix. What is the end goal of this?

[LacquerHed]

Trying to export a raw expression matrix to feed into a shiny app for web hosting the data. Easy enough with individual biological replicates but trying to figure out how to export the merged raw data etc. The following are things needed to build the site (from github tutorial):

subset_GSE72857.txt: Raw gene expression matrix, with column as cells and rows as genes, rownames must be unique.
subset_GSE72857_log2norm.txt: Log2 normalized expression matrix, same dimension as raw matrix. You can also input any other type of normalized data as long as it matches the dimension of raw data.
subset_GSE72857_pmeta.txt: Meta data for the cells.

https://github.com/qinzhu/VisCello

Thanks

[ATpoint]

I guess https://rdrr.io/github/satijalab/seurat/man/GetAssay.html will allow to get the assay, and from there you can convert to any format you like, e.g. using the Matrix package, if the assay is not already the sparse format you want.