Enable genome parameter to be a string; #1437

stuart-lab · Jun 28, 2023 · 2d7ac60 · 2d7ac60
1 parent 2ad6c3c
commit 2d7ac60
Showing 1 changed file with 8 additions and 0 deletions.
diff --git a/R/motifs.R b/R/motifs.R
@@ -29,6 +29,14 @@ AddMotifs.default <- function(
   if (verbose) {
     message("Building motif matrix")
   }
+  # genome can be string
+  if (is.character(x = genome)) {
+    if (!requireNamespace("BSgenome", quietly = TRUE)) {
+      stop("Please install BSgenome.
+             https://www.bioconductor.org/packages/BSgenome/")
+    }
+    genome <- BSgenome::getBSgenome(genome = genome)
+  }
   motif.matrix <- CreateMotifMatrix(
     features = object,
     pwm = pfm,