diff --git a/DESCRIPTION b/DESCRIPTION index f35ef50..93b077e 100644 --- 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 index b94e711..889ca53 100644 --- 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") {