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dmcable / spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
GNU General Public License v3.0
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DE genes for cell-types #39

Closed Roopali24 closed 3 years ago

Roopali24 commented 3 years ago

Hi,

I have a question regarding the DE genes produced by RCTD. I can see that the list of DE genes is saved in myRCTD@internal_vars$gene_list_reg but I want to know which of the genes are specific to a certain cell type as the output shows things like: [1] "get_de_genes: Astrocytes found DE genes: 176" [1] "get_de_genes: Bergmann found DE genes: 232" [1] "get_de_genes: Choroid found DE genes: 217" [1] "get_de_genes: Endothelial found DE genes: 354"

So I want to know those Astrocyte or Endothelial specific genes and not just the total DE genes. Can you please tell me if that information is saved with the results.

Thank you, Roopali

dmcable commented 3 years ago

Hi Roopali,

This information isn't used directly by RCTD; however, it is possible to access this information. The gene expression matrix is in myRCTD@cell_type_info$info[[1]]. There, for each gene you can tell which cell type expresses it the most. Alternatively, you can use the get_marker_data function, as in the following script:

https://raw.githack.com/dmcable/RCTD/dev/AnalysisPaper/MainFigures/figure4.html

In this case, you could call: get_marker_data(myRCTD@cell_type_info$info[[2]], myRCTD@cell_type_info$info[[1]], myRCTD@internal_vars$gene_list_bulk)

Hope this helps!