From 2afd52df21e4e1dff1a5af5f52d70dabcff47e86 Mon Sep 17 00:00:00 2001 From: Bioconductor Git-SVN Bridge Date: Mon, 13 Oct 2014 10:35:54 -0700 Subject: [PATCH 1/2] Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit. Commit information: SVN Revision number: 95404 Commit message: Corrected formatting of the NEWS file. This is not a free-form text file, it must be formatted correctly if you want the latest NEWS to appear in the Bioconductor release announcement. Committed by d.tenenbaum Committed at: 2014-10-13T17:34:04.204390Z --- NEWS | 50 +++++++++++++++++++++++++++++++------------------- data/.Rhistory | 23 ----------------------- 2 files changed, 31 insertions(+), 42 deletions(-) delete mode 100644 data/.Rhistory diff --git a/NEWS b/NEWS index fe3d7f9..7fed270 100644 --- a/NEWS +++ b/NEWS @@ -1,26 +1,38 @@ -Version 1.99.3 -------------------------------------------------------------------------------- -* Bumped the version number to 1.99.3 +CHANGES IN VERSION 1.99.3 +------------------------- -Version 0.99.3 -------------------------------------------------------------------------------- -* Updated Vignette to biocStyle -* Form now GOsummaries is going to live in Bioconductor and this version supersedes the CRAN version 1.1 +CHANGES -Version 0.99.2 -------------------------------------------------------------------------------- -* Reformatted code for Bioconductor -* Improved Vignette + o Bumped the version number to 1.99.3 +CHANGES IN VERSION 0.99.3 +-------------------------- -Version 1.1 -------------------------------------------------------------------------------- -* Added support for custom data in word clouds (see gosummaries functions) -* Now it is possible to display genes instead of GO categories (see show_genes parameter in gosummaries.MArrayLM, gosummaries.prcomp and gosummaries.matrix) -* Added function gosummaries.matrix that takes in a matrix that is a MDS representation of data and expression matrix and then finds most correlated features for each MDS component. +NEW FEATURES -Version 1.0 -------------------------------------------------------------------------------- -First version of the package + o Updated Vignette to biocStyle + o Form now GOsummaries is going to live in Bioconductor and this version supersedes the CRAN version 1.1 +CHANGES IN VERSION 0.99.2 +-------------------------- + +NEW FEATURES + + o Reformatted code for Bioconductor + o Improved Vignette + + +CHANGES IN VERSION 1.1 +---------------------- + + o Added support for custom data in word clouds (see gosummaries functions) + o Now it is possible to display genes instead of GO categories (see show_genes parameter in gosummaries.MArrayLM, gosummaries.prcomp and gosummaries.matrix) + o Added function gosummaries.matrix that takes in a matrix that is a MDS representation of data and expression matrix and then finds most correlated features for each MDS component. + +CHANGES IN VERSION 1.0 +---------------------- + +NEW FEATURES + + o First version of the package diff --git a/data/.Rhistory b/data/.Rhistory deleted file mode 100644 index 3e248a6..0000000 --- a/data/.Rhistory +++ /dev/null @@ -1,23 +0,0 @@ -load("/Users/Kolde/Raivo/Projects/GOsummaries/GOsummaries/data/lukk_small.RData") -load("/Users/Kolde/Raivo/Projects/GOsummaries/Data/testlukk.RData") -sl -ls() -ehad(testlukk) -str(testlukk) -str(lukk_small) -library(plyr) -data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)) -daply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, 6)) -daply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, sample(5:6, 1))) -dlply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, 6)) -unlist(dlply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, 6))) -e = lukk_small$exp[] -i = unlist(dlply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, 6))) -e = lukk_small$exp[i, ] -a = lukk_small$annot[i, ] -e = lukk_small$exp[, i] -dim(e) -dim(a) -tissue_example = list(exp = e, annot = a) -save(tissue_exampe, file = "~/Raivo/Projects/GOsummaries/GOsummaries/data/tissue_examples.RData") -save(tissue_example, file = "~/Raivo/Projects/GOsummaries/GOsummaries/data/tissue_examples.RData") From 9b0ab3e246795175e0acbbdae0bdd82fc5779f55 Mon Sep 17 00:00:00 2001 From: Bioconductor Git-SVN Bridge Date: Mon, 13 Oct 2014 14:53:21 -0700 Subject: [PATCH 2/2] Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commits. Commit information: SVN Revision number: 95439 Commit message: Bump package versions prior to creating the 3.0 branch. Committed by d.tenenbaum Committed at: 2014-10-13T21:38:33.867451Z SVN Revision number: 95443 Commit message: Bumping versions after creating 3.0 release branch. Committed by d.tenenbaum Committed at: 2014-10-13T21:47:41.382147Z --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 159ea7a..ad54c24 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: GOsummaries -Version: 1.99.3 +Version: 2.1.0 Date: 2014-09-29 License: GPL (>= 2) Description: A package to visualise Gene Ontology (GO) enrichment analysis