@@ -3105,7 +3105,12 @@ filterGRNAndConnectGenes <- function(GRN,

     if (filterLoops) {

       futile.logger::flog.info(paste0(" Filter TF-TF self-loops"))

       futile.logger::flog.info(paste0("  Number of rows before filtering genes: ", nrow(grn.filt)))

-      grn.filt = dplyr::filter(grn.filt, as.character(.data$gene.ENSEMBL) != as.character(.data$TF.ENSEMBL))

+      

+      # Be aware of NA values here in the selection, depending on allowMissingTFs

+      grn.filt = dplyr::filter(grn.filt, 

+                               is.na(.data$TF.ENSEMBL) | 

+                               (!is.na(.data$TF.ENSEMBL) & (as.character(.data$gene.ENSEMBL) != as.character(.data$TF.ENSEMBL))))

+      

       futile.logger::flog.info(paste0("  Number of rows after filtering genes: ", nrow(grn.filt)))

     }