update BgeeDB_manual - comment on biomart

tests/testthat/test_list_annotation_output.R

@@ -3,7 +3,7 @@ context("expect_output")
 
 test_that("Annotation files", {
   bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
-  annotation_bgee_mouse <- getAnnotation()
+  annotation_bgee_mouse <- getAnnotation(bgee)
 
 
   expect_that( annotation_bgee_mouse, is_a("list") )

vignettes/BgeeDB_Manual.Rmd

@@ -154,8 +154,8 @@ The strigency on the quality of expression calls can be changed with the ```conf
 First we need to prepare a list of genes in the foreground and in the background. The input format is the same as the gene list required to build a ```topGOdata``` object in the ```topGO``` package: a vector with background genes as names, and 0 or 1 values depending if a gene is in the foreground or not. In this example we will look at genes, annotated with "spermatogenesis" in the Gene Ontology (using the ```biomaRt``` package). We expect these genes to be enriched for expression in male tissues, notablythe testes. The background list of genes is set to all genes annotated to at least one Gene Ontology term, allowing to account for biases in which types of genes are more likely to receive Gene Ontology annotation.
 
 ```{r}
-source("https://bioconductor.org/biocLite.R")
-biocLite("biomaRt")
+# source("https://bioconductor.org/biocLite.R")
+# biocLite("biomaRt")
 library(biomaRt)
 ensembl <- useMart("ensembl")
 ensembl <- useDataset("drerio_gene_ensembl", mart=ensembl)