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scGPT/Redeconve/Redeconve_PDAC.R

+# devtools::install_github("ZxZhou4150/Redeconve", build_vignettes = F)
+library(Redeconve)
+# data(basic)
+library(Matrix)
+# library(Matrix.utils)
+load("./PDAC/basic.RData")
+
+data_folder <- "./PDAC/"
+
+
+annotations <- read.csv(paste0(data_folder, "./annotations.csv"))
+
+# ref <- get.ref(sc, annotations, dopar = F)
+
+# res.ct <- deconvoluting(ref, sp, genemode = "def", hpmode = "auto", dopar = T, ncores = 8)
+
+
+idx <- cell.sampling(ncells = 100064, annotations, size = 1000, prot = T)
+sc.ds <- sc[, idx[, 1]]
+
+res.ds <- deconvoluting(sc.ds, st, genemode = "def", hpmode = "def", dopar = T, ncores = 32)
+write.csv(as.matrix(res.ds), "Redeconve_human_breast.csv")