I'm trying to do a cross-species comparison between the patient TME vs. the PTX TME to understand gene expression conservation. I have already converted between mouse and human genes giving me a resultant gene expression matrix that is just one set of (homologous) genes X cells for all mouse and human cells.

musGenes <- rownames(mouse_only)
# Basic function to convert mouse to human gene names
convertMouseGeneList <- function(x){
h = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
m = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
genesV2 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = x , mart = m, attributesL = c("hgnc_symbol"), martL = h, uniqueRows=T)
humanx <- unique(genesV2[, 2])
# Print the first 6 genes found to the screen
genes <- convertMouseGeneList(musGenes)

Now how do I create a new Seurat object with the converted mouse gene list, such as rename the matrix, so that the rownames/colnames are human symbols, rather than mouse symbols?

  • 1
    $\begingroup$ is this thread useful? They do rename rownames of the just created seurat object. $\endgroup$
    – gabt
    Aug 23 at 11:08

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