bugfix (b77f9b4e) · Commits · github_fork / HdWGCNA

Figure5_project_modules.Rmd

+1142 −4

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+5 −3

Original line number	Diff line number	Diff line
		@@ -517,8 +517,7 @@ ComputeModuleEigengene <- function(
		}

		# get genes in this module:
		cur_genes <- modules %>% subset(module == cur_mod) %>% .$gene_name
		print(cur_genes)
		cur_genes <- modules %>% subset(module == cur_mod) %>% .$gene_name %>% as.character()

		# subset seurat object by these genes only:
		X_dat <- GetAssayData(seurat_obj, slot='data', assay = assay)[cur_genes,]
		@@ -646,7 +645,7 @@ ModuleEigengenes <- function(
		verbose=TRUE,
		assay = NULL,
		pc_dim = 1,
		exclude_grey = TRUE,
		exclude_grey = FALSE,
		wgcna_name=NULL, ...
		){

		@@ -668,6 +667,9 @@ ModuleEigengenes <- function(
		stop(paste0("Normalized data slot not found in selected assay ", assay))
		}

		# exclude grey doesn't work yet:
		if(exclude_grey){exclude_grey <- FALSE}


		me_list <- list()
		harmonized_me_list <- list()