diff --git a/README.md b/README.md index 16f71fa..b7d54b4 100644 --- a/README.md +++ b/README.md @@ -32,23 +32,23 @@ data(motifs) seurat_object <- Seurat::FindVariableFeatures(seurat_object, assay='RNA') # Initiate GRN object and select candidate regions -seurat_object <- initiate_grn(seurat_object) +grn_object <- initiate_grn(seurat_object) # Scan candidate regions for TF binding motifs -seurat_object <- find_motifs( - seurat_object, +grn_object <- find_motifs( + grn_object, pfm = motifs, genome = BSgenome.Hsapiens.UCSC.hg38 ) # Infer gene regulatory network -seurat_object <- infer_grn(seurat_object) +grn_object <- infer_grn(grn_object) # Print inferred coefficients -coef(seurat_object) +coef(grn_object) # Find gene and regulatory modules -test_srt <- find_modules(test_srt) +test_srt <- find_modules(grn_object) # Print modules NetworkModules(test_srt)