Speed improvements on getGAF

ropensci · Dec 13, 2023 · 05df47b · 05df47b
1 parent 10bd65c
commit 05df47b
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,7 @@
  relations).
 * New `dimnames()` and `names()` functions to discover the names of the data in 
  the slots.
+* Minor changes to `getGAF()` to improve speed.
 
 # BaseSet 0.9.0
 

diff --git a/R/obo.R b/R/obo.R
@@ -118,17 +118,18 @@ getGAF <- function(x) {
 
     # Modify if they are GeneOntolgoy
     GO <- grepl("^GO:", df$O_ID)
-    df$Aspect[GO] <- gsub("P", "BP", df$Aspect[GO])
-    df$Aspect[GO] <- gsub("C", "CC", df$Aspect[GO])
-    df$Aspect[GO] <- gsub("F", "MF", df$Aspect[GO])
+    df$Aspect[GO] <- gsub("P", "BP", df$Aspect[GO], fixed = TRUE)
+    df$Aspect[GO] <- gsub("C", "CC", df$Aspect[GO], fixed = TRUE)
+    df$Aspect[GO] <- gsub("F", "MF", df$Aspect[GO], fixed = TRUE)
 
     # Classification of the columns according to where do they belong
     elements <- c(1, 2, 3, 10, 11, 12, 13, 17)
     sets <- c(5, 6, 9, 16)
 
     # Change the name of the columns to be ready to use tidySet.data.frame
-    colnames(df) <- gsub("O_ID", "sets", colnames(df))
-    colnames(df) <- gsub("DB_Object_Symbol", "elements", colnames(df))
+    colnames(df) <- gsub("O_ID", "sets", colnames(df), fixed = TRUE)
+    colnames(df) <- gsub("DB_Object_Symbol", "elements", colnames(df),
+                         fixed = TRUE)
 
     TS <- tidySet(df)