Merge pull request #28 from hpages/master

Replace GenomicFeatures::makeTxDbFromGFF with txdbmaker::makeTxDbFromGFF
FelixErnst · Mar 26, 2024 · 184805d · 184805d
2 parents 7423101 + 51dcdb4
commit 184805d
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diff --git a/R/normalization.R b/R/normalization.R
@@ -42,7 +42,7 @@ NULL
            call. = FALSE)
     }
     if(!is(annotation,"TxDb")){
-      annotation <- GenomicFeatures::makeTxDbFromGFF(annotation)
+      annotation <- txdbmaker::makeTxDbFromGFF(annotation)
     }
   } else {
     annotation <- .norm_annotation_GRangesList(annotation)

diff --git a/vignettes/RNAmodR.Rmd b/vignettes/RNAmodR.Rmd
@@ -59,6 +59,7 @@ suppressPackageStartupMessages({
   library(rtracklayer)
   library(Rsamtools)
   library(GenomicFeatures)
+  library(txdbmaker)
   library(RNAmodR.Data)
   library(RNAmodR)
 })
@@ -67,6 +68,7 @@ suppressPackageStartupMessages({
 library(rtracklayer)
 library(Rsamtools)
 library(GenomicFeatures)
+library(txdbmaker)
 library(RNAmodR.Data)
 library(RNAmodR)
 ```