update DESCRIPTION, Bgee.R, added NEWS.Rd to inst/, update test_forma…

…t_data, update BgeeDB_Manual

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: BgeeDB
 Type: Package
 Title: Annotation and gene expression data from Bgee database
-Version: 0.99.5
+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.
 Depends:
-    R (>= 3.0),
+    R (>= 3.3),
     topGO,
     tidyr
 Imports:
@@ -25,7 +25,6 @@ VignetteBuilder: knitr
 biocViews: Software, DataImport, Sequencing, GeneExpression, Microarray, GO
 Suggests:
     knitr,
-    dplyr,
     BiocStyle,
     testthat,
     rmarkdown

R/Bgee.R

@@ -29,7 +29,7 @@
     expr.final <- lapply(expr, function(x) x %>% spread("Chip ID", "Log of normalized signal intensity"))
 
   }
-  expr.final <- as.data.frame(expr.final[[1]])
+
   return(expr.final)
 
 }

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_format_data.R

@@ -6,7 +6,7 @@ test_that("Formatting gene expression files", {
   data_bgee_mouse_exp <- bgee$get_data(experiment.id  = "GSE30617")
   gene.expression <- bgee$format_data(data_bgee_mouse_exp, calltype = "expressed", stats = "rpkm")
 
-  expect_that( gene.expression, is_a("data.frame") )
-  expect_true( colnames(gene.expression)[1] == "Gene ID" )
+  expect_that( gene.expression, is_a("list") )
+  expect_true( colnames(gene.expression[[1]])[1] == "Gene ID" )
 
 })

vignettes/BgeeDB_Manual.Rmd

@@ -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