From 721af032c72d643b00cd35ecc7e48f7b08f12653 Mon Sep 17 00:00:00 2001 From: wirawara Date: Tue, 11 Oct 2016 17:14:54 +0200 Subject: [PATCH] update BgeeDB_manual - comment on biomart --- tests/testthat/test_list_annotation_output.R | 2 +- vignettes/BgeeDB_Manual.Rmd | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/testthat/test_list_annotation_output.R b/tests/testthat/test_list_annotation_output.R index 829d3e4..3a36a03 100644 --- a/tests/testthat/test_list_annotation_output.R +++ b/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") ) diff --git a/vignettes/BgeeDB_Manual.Rmd b/vignettes/BgeeDB_Manual.Rmd index 8e04580..750718c 100644 --- a/vignettes/BgeeDB_Manual.Rmd +++ b/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)