Merge pull request #24 from hpages/devel

The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
leekgroup · Mar 26, 2024 · 4d91870 · 4d91870
2 parents 742c5ea + e95d6fb
commit 4d91870
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -45,6 +45,7 @@ Suggests:
     sessioninfo,
     EnsDb.Hsapiens.v79,
     GenomicFeatures,
+    txdbmaker,
     knitr (>= 1.6),
     org.Hs.eg.db,
     RefManageR,

diff --git a/R/reproduce_ranges.R b/R/reproduce_ranges.R
@@ -64,6 +64,7 @@ reproduce_ranges <- function(level = "gene", db = "Gencode.v25") {
     ## Load required packages
     .load_check(c("GenomicFeatures", "org.Hs.eg.db"))
     if (db == "Gencode.v25") {
+        .load_check("txdbmaker")
         temp_gencode <- file.path(
             tempdir(),
             "gencode.v25.annotation.gff3.gz"
@@ -75,7 +76,7 @@ reproduce_ranges <- function(level = "gene", db = "Gencode.v25") {
             ),
             destfile = temp_gencode
         )
-        txdb <- GenomicFeatures::makeTxDbFromGFF(temp_gencode,
+        txdb <- txdbmaker::makeTxDbFromGFF(temp_gencode,
             format = "gff3", organism = "Homo sapiens"
         )
     } else if (db == "EnsDb.Hsapiens.v79") {