better information about summarize: assignRanges

thelovelab · Jun 8, 2024 · ccf9675 · ccf9675
1 parent 7b618e5
commit ccf9675
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: tximeta
-Version: 1.23.1
+Version: 1.23.2
 Title: Transcript Quantification Import with Automatic Metadata
 Description: Transcript quantification import from Salmon and
     other quantifiers with automatic attachment of transcript ranges

diff --git a/R/summarizeToGene.R b/R/summarizeToGene.R
@@ -50,9 +50,11 @@ summarizeToGene.SummarizedExperiment <- function(object,
 
   # note here about how ranges are assigned
   if (assignRanges == "abundant") {
-    message("gene ranges assigned by isoform abundance, see `assignRanges`")
+    message("assignRanges='abundant': gene ranges assigned by isoform abundance
+  see details at: ?summarizeToGene,SummarizedExperiment-method")
   } else {
-    message("gene ranges assigned by total range of isoforms, see `assignRanges`")
+    message("assignRanges='range': gene ranges assigned by total range of isoforms
+  see details at: ?summarizeToGene,SummarizedExperiment-method")
   }
 
   txi.gene <- summarizeToGene(object=txi, tx2gene=tx2gene, varReduce=varReduce, ...)

diff --git a/R/tximeta.R b/R/tximeta.R
@@ -47,11 +47,10 @@
 #'
 #' @author Michael I. Love, Charlotte Soneson, Peter Hickey, Rob Patro
 #' 
-#' @docType package
 #' @name tximeta-package
 #' @aliases tximeta-package
 #' @keywords package
-NULL
+"_PACKAGE"
 
 #' Import transcript quantification with metadata
 #'