run_Seurat <- function(cells.1, cells.2, method = "bimod") {
message(paste("Seurat", method))
session_info <- sessionInfo()
tryCatch({
timing <- system.time({
umicount <- mat.raw
umicount <- umicount[, c(cells.1, cells.2)]
colnames(umicount) <- c(rep("cond", length(cells.1)), rep("noncond", length(cells.2)))
colnames(umicount) <- paste0(colnames(umicount), "__", 1:ncol(umicount))
seur <- Seurat::CreateSeuratObject(counts = umicount, project = "scrnaseq",
names.field = 1, names.delim = "__")
res <- Seurat::FindMarkers(seur, ident.1 = "cond",
ident.2 = "noncond", test.use = method, logfc.threshold = -1)
})
list(session_info = session_info,
timing = timing,
res = res,
df = data.frame(pval = res$p_val,
padj = p.adjust(res$p_val, method = "BH"),
row.names = rownames(res)))
}, error = function(e) {
"Seurat results could not be calculated"
list(session_info = session_info)
})
}
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