1. SplicingGraphs
  2. Commit 3cf026efc51d30ce5b29dfe95810f1dc42e1fb72
Browse code

follow renaming of makeTranscriptDb*() functions to makeTxDb*()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@95795 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 20/10/2014 18:55:58
Showing 4 changed files
DESCRIPTION
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 Package: SplicingGraphs
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 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads
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 	to them
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-Version: 1.7.0
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+Version: 1.7.1
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 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
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 License: Artistic-2.0
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 Description: This package allows the user to create, manipulate, and visualize
inst/unitTests/test_countReads-methods.R
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 {
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      library(GenomicFeatures)
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      suppressWarnings(
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-       toy_genes_txdb <- makeTranscriptDbFromGFF(toy_genes_gff())
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+       toy_genes_txdb <- makeTxDbFromGFF(toy_genes_gff())
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      )
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      SplicingGraphs(toy_genes_txdb)
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 }
man/SplicingGraphs-class.Rd
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@@ -234,7 +234,7 @@ SplicingGraphs(x, grouping=NULL, min.ntx=2, max.ntx=NA, check.introns=TRUE)
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 library(GenomicFeatures)
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 suppressWarnings(
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-  toy_genes_txdb <- makeTranscriptDbFromGFF(toy_genes_gff())
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+  toy_genes_txdb <- makeTxDbFromGFF(toy_genes_gff())
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 )
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 ## ---------------------------------------------------------------------
man/toy_data.Rd
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@@ -40,7 +40,7 @@ toy_overlaps()
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           \link[GenomicAlignments]{GAlignmentPairs} classes defined
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           in the \pkg{GenomicAlignments} package.
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-    \item The \code{\link[GenomicFeatures]{makeTranscriptDbFromGFF}}
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+    \item The \code{\link[GenomicFeatures]{makeTxDbFromGFF}}
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           function and the \link[GenomicFeatures]{TxDb} class
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           defined in the \pkg{GenomicFeatures} package.
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   }
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@@ -57,7 +57,7 @@ cat(readLines(toy_genes_gff()), sep="\n")
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 library(GenomicFeatures)
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 suppressWarnings(
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-  txdb <- makeTranscriptDbFromGFF(toy_genes_gff())
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+  txdb <- makeTxDbFromGFF(toy_genes_gff())
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 )
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 ## Plot all the transcripts in the gene model: