[med-svn] [r-bioc-cummerbund] 01/03: Imported Upstream version 2.4.1

[Andreas Tille]

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commit 170677487d3b16de7f0fe7e3bb71253e3b47a6a0
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 28 17:24:34 2013 +0100

    Imported Upstream version 2.4.1
---
 DESCRIPTION                              |   4 ++--
 build/vignette.rds                       | Bin 0 -> 302 bytes
 inst/doc/cummeRbund-example-workflow.pdf | Bin 198250 -> 198250 bytes
 inst/doc/cummeRbund-manual.R             |   2 +-
 inst/doc/cummeRbund-manual.Rnw           |   2 +-
 inst/doc/cummeRbund-manual.pdf           | Bin 1545261 -> 1545258 bytes
 6 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 64b4663..24271c3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: cummeRbund
 Title: Analysis, exploration, manipulation, and visualization of
         Cufflinks high-throughput sequencing data.
-Version: 2.2.0
+Version: 2.4.1
 Date: 2012-05-04
 Author: L. Goff, C. Trapnell, D. Kelley
 Description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data.  In addition, provides numerous plotting functions for commonly used visualizations.
@@ -20,4 +20,4 @@ biocViews: HighThroughputSequencing, HighThroughputSequencingData,
         RNAseq, RNAseqData, GeneExpression, DifferentialExpression,
         Infrastructure, DataImport, DataRepresentation, Visualization,
         Bioinformatics, Clustering, MultipleComparisons, QualityControl
-Packaged: 2013-04-04 08:23:26 UTC; biocbuild
+Packaged: 2013-12-13 05:38:16 UTC; biocbuild
diff --git a/build/vignette.rds b/build/vignette.rds
new file mode 100644
index 0000000..08663be
Binary files /dev/null and b/build/vignette.rds differ
diff --git a/inst/doc/cummeRbund-example-workflow.pdf b/inst/doc/cummeRbund-example-workflow.pdf
index 5540834..9642067 100644
Binary files a/inst/doc/cummeRbund-example-workflow.pdf and b/inst/doc/cummeRbund-example-workflow.pdf differ
diff --git a/inst/doc/cummeRbund-manual.R b/inst/doc/cummeRbund-manual.R
index 41d08cf..ffb4ed8 100644
--- a/inst/doc/cummeRbund-manual.R
+++ b/inst/doc/cummeRbund-manual.R
@@ -549,7 +549,7 @@ biomTrack<-BiomartGeneRegionTrack(genome=genome,chromosome=as.character(myChr),
 trackList<-c(trackList,biomTrack)
  
 conservation <- UcscTrack(genome = genome, chromosome = myChr,
-		track = "Conservation", table = "phyloP46wayPlacental",
+		track = "Conservation", table = "phyloP100wayAll",
 		from = myStart-2000, to = myEnd+2000, trackType = "DataTrack",
 		start = "start", end = "end", data = "score",
 		type = "hist", window = "auto", col.histogram = "darkblue",
diff --git a/inst/doc/cummeRbund-manual.Rnw b/inst/doc/cummeRbund-manual.Rnw
index d1e69a7..25de050 100644
--- a/inst/doc/cummeRbund-manual.Rnw
+++ b/inst/doc/cummeRbund-manual.Rnw
@@ -929,7 +929,7 @@ biomTrack<-BiomartGeneRegionTrack(genome=genome,chromosome=as.character(myChr),
 trackList<-c(trackList,biomTrack)
  
 conservation <- UcscTrack(genome = genome, chromosome = myChr,
-		track = "Conservation", table = "phyloP46wayPlacental",
+		track = "Conservation", table = "phyloP100wayAll",
 		from = myStart-2000, to = myEnd+2000, trackType = "DataTrack",
 		start = "start", end = "end", data = "score",
 		type = "hist", window = "auto", col.histogram = "darkblue",
diff --git a/inst/doc/cummeRbund-manual.pdf b/inst/doc/cummeRbund-manual.pdf
index 63cc480..3fde9f0 100644
Binary files a/inst/doc/cummeRbund-manual.pdf and b/inst/doc/cummeRbund-manual.pdf differ

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