Merge remote-tracking branch 'upstream/master'

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: BgeeDB
 Type: Package
 Title: Annotation and gene expression data from Bgee database
-Version: 0.99.4
+Version: 0.99.6
 Date: 2016-03-15
 Author: Andrea Komljenovic [aut, cre], Julien Roux [aut, cre]
-Maintainer: Andrea Komljenovic  <andreakomljenovic@gmail.com>, Frédéric Bastian <bgee@sib.swiss>
+Maintainer: Andrea Komljenovic  <andreakomljenovic@gmail.com>, Frederic Bastian <bgee@sib.swiss>
 Description: A package for the annotation and gene expression
     data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms,
     mapped to genes by expression patterns.
@@ -18,6 +18,7 @@ Imports:
     methods,
     stats,
     utils,
+    dplyr,
     graph
 License: GPL-2
 VignetteBuilder: knitr

NAMESPACE

@@ -13,4 +13,5 @@ import(methods)
 import(stats)
 import(topGO)
 import(utils)
+importFrom(dplyr,"%>%")
 importFrom(tidyr,spread)

R/listBgeeSpecies.R

@@ -35,7 +35,7 @@ listBgeeSpecies <- function(...){
   df.species.db <- data.frame(ID = species.taxid, GENUS = genus.name, SPECIES = species.name, COMMON = common.name)
 
   cat("Last update:" , .listDirectories(url_rnaseq, version = TRUE), "\n")
-	return(list("Species in the Database"= df.species.db, RNAseq = .listDirectories(url_rnaseq), Affymetrix = .listDirectories(url_affymetrix)))
+	return(list("Species in the Database"= df.species.db, "RNAseq" = .listDirectories(url_rnaseq), "Affymetrix" = .listDirectories(url_affymetrix)))
 
 }
 

README.md

@@ -31,11 +31,15 @@ In the terminal:
 
     git clone https://github.com/BgeeDB/BgeeDB_R.git
 
+Then in R:
+``` {r}
+install.packages("./BgeeDB", repos = NULL, type="source")
+```
 Or, download the project (`master` branch) by clicking the `Download ZIP` button on the web interface, and unzip it.
 
 Then in R:
 ``` {r}
-install.packages("./BgeeDB", repos = NULL, type="source")
+install.packages("./BgeeDB-master", repos = NULL, type="source")
 ```
 
 ### Install via install\_github()

inst/CITATION

@@ -6,12 +6,10 @@ citHeader("To cite reports in publications, please use:")
 citEntry(entry = "manual",
     title = "BgeeDB: an R package for annotation and gene expression data retrieval from Bgee database",
     author = personList( as.person("Andrea Komljenovic"), as.person("Julien Roux")),
-    note = "version 0.99.0",
     year = "2016",
     url = "http://github.com/wirawara/BgeeDB",
     textVersion  = paste("Komljenovic A, Roux J (2016).",
-        "BgeeDB: an R package for annotation and gene expression data retrieval from Bgee database.",
-        "version 0.99.4")
+        "BgeeDB: an R package for annotation and gene expression data retrieval from Bgee database.")
 )
 
 citEntry(entry="Article",

inst/NEWS.Rd

@@ -0,0 +1,36 @@
+\name{NEWS}
+\title{News for Package \pkg{BgeeDB}}
+
+\section{Changes in version 0.99.6 (2016-04-28)}{
+  \itemize{
+    \item  Bug fix in format_data function.
+  }
+}
+
+\section{Changes in version 0.99.4 (2016-04-26)}{
+  \itemize{
+    \item  Bug fix for Affymetrix data.
+  }
+}
+
+\section{Changes in version 0.99.3 (2016-04-22)}{
+  \itemize{
+    \item  Added download for Affymetrix data.
+  }
+}
+
+
+\section{Changes in version 0.0.4 (2016-03-20)}{
+  \itemize{
+    \item  Added loadTopAnatData function.
+  }
+}
+
+\section{Changes in version 0.0.1 (2016-03-13)}{
+  \itemize{
+    \item Added topAnat script.
+      This function produces a topAnatObject,
+      ready to use for gene set enrichment testing
+      using functions from the topGO package
+  }
+}

tests/testthat/test_list_annotation_output.R

@@ -10,5 +10,5 @@ test_that("Annotation files", {
   expect_that( length(annotation_bgee_mouse), equals(2) )
   expect_that( unique(names(annotation_bgee_mouse) %in% c("experiment_annotation", "sample_annotation")), is_true() )
   expect_message(message("Saved files "))
-  expect_true(dir.exists(file.path("..", "Mus_musculus")))
+  # expect_true(dir.exists(file.path("..", "Mus_musculus")))
 })

vignettes/BgeeDB_Manual.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "BgeeDB: an R package for datasets retrieval from Bgee database"
-author: "Andrea Komljenović, Julien Roux, Marc Robinson-Rechavi, Frédéric Bastian"
+author: "Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic Bastian"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
@@ -82,7 +82,7 @@ Alternatively, you can choose to download only one experiment from Bgee, as in t
 data_bgee_mouse_gse30617 <- bgee$get_data(experiment.id = "GSE30617")
 ```
 
-The data from different samples will be listed in rows, one after the other. It is sometimes easier to work with data organized as a matrix, where different columns represent different samples. To transform the data into a matrix with genes in rows and samples in columns, you can use the ```bgee$format_data()``` function. This function also allows to filter out genes that are not called present in a given sample (giving them NA values).
+The data from different samples will be listed in rows, one after the other. It is sometimes easier to work with data organized as a matrix, where different columns represent different samples. To transform the data into a matrix with genes in rows and samples in columns, you can use the ```bgee$format_data()``` function that separates data according to anatomical term. This function also allows to filter out genes that are not called present in a given sample (giving them NA values).
 
 ```{r}
 # only present calls and rpkm values for GSE30617