From 9d4947d895218844c51e1635d602b64ad2e7987c Mon Sep 17 00:00:00 2001 From: wirawara Date: Fri, 29 Apr 2016 00:51:00 +0200 Subject: [PATCH] update DESCRIPTION, Bgee.R, added NEWS.Rd to inst/, update test_format_data, update BgeeDB_Manual --- DESCRIPTION | 7 +++--- NEWS | 7 ------ R/Bgee.R | 2 +- inst/NEWS.Rd | 36 +++++++++++++++++++++++++++++++ tests/testthat/test_format_data.R | 4 ++-- vignettes/BgeeDB_Manual.Rmd | 2 +- 6 files changed, 43 insertions(+), 15 deletions(-) delete mode 100644 NEWS create mode 100644 inst/NEWS.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 511b7ef..31e017e 100644 --- a/DESCRIPTION +++ b/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 , Frédéric Bastian +Maintainer: Andrea Komljenovic , Frederic Bastian 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 diff --git a/NEWS b/NEWS deleted file mode 100644 index d9874d5..0000000 --- a/NEWS +++ /dev/null @@ -1,7 +0,0 @@ -CHANGES IN VERSION 0.0.1 -========================= - - o Added topAnat script. - This function produces a topAnatObject, - ready to use for gene set enrichment testing - using functions from the topGO package diff --git a/R/Bgee.R b/R/Bgee.R index e849ce4..bcbbbf2 100644 --- a/R/Bgee.R +++ b/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) } diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd new file mode 100644 index 0000000..a98130f --- /dev/null +++ b/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 + } +} diff --git a/tests/testthat/test_format_data.R b/tests/testthat/test_format_data.R index 55ec7d3..58c2db7 100644 --- a/tests/testthat/test_format_data.R +++ b/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" ) }) diff --git a/vignettes/BgeeDB_Manual.Rmd b/vignettes/BgeeDB_Manual.Rmd index d8fb0b7..873f2ec 100644 --- a/vignettes/BgeeDB_Manual.Rmd +++ b/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