Shamoun was interested in finding coexpressed genes in specific cell types. Here is some code to do that. You have to enter in each cell type of interest individually.
# Create a variable called 'sce' that contains our Large SingleCellExperiment object from a file using R function readRDS() sce <- readRDS(file = "~/workspace/Storage/C_MOOR/c_moor_ccc_su22/gastrulation_sce.RDS") # Find top variable genes sce <- logNormCounts(sce) colLabels(sce) <- factor(sce$celltype) dec <- modelGeneVar(sce) top.hvgs <- getTopHVGs(dec, n=2000) # Create a variable with your favorite gene my_favorite_genes <- c("ENSMUSG00000038192","ENSMUSG00000047139") # Create a variable with your favorite genes included together with the top HVGs of.interest <- c(top.hvgs[1:200], my_favorite_genes) # Subset dataset to just the celltypes you are interested in sce_subset <- sce[,sce$celltype %in% c("Def. endoderm")] cor.pairs <- correlatePairs(x = sce_subset, subset.row = of.interest) cor.pairs