## ----------------------------------------------------------------------------- #if (!requireNamespace("BiocManager", quietly=TRUE)) #install.packages("BiocManager") #BiocManager::install("BgeeDB") ## ----message = FALSE, warning = FALSE----------------------------------------- library(BgeeDB) ## ----------------------------------------------------------------------------- listBgeeSpecies() ## ----------------------------------------------------------------------------- listBgeeSpecies(release = "13.2", order = 2) ## ----------------------------------------------------------------------------- bgee <- Bgee$new(species = "Danio_rerio", dataType = "rna_seq") ## ----------------------------------------------------------------------------- annotation_bgee_zebrafish <- getAnnotation(bgee) # list the first experiments and libraries lapply(annotation_bgee_zebrafish, head) ## ----------------------------------------------------------------------------- # download all RNA-seq experiments from zebrafish data_bgee_zebrafish <- getSampleProcessedData(bgee) # number of experiments downloaded length(data_bgee_zebrafish) # check the downloaded data lapply(data_bgee_zebrafish, head) # isolate the first experiment data_bgee_experiment1 <- data_bgee_zebrafish[[1]] ## ----------------------------------------------------------------------------- # download data for GSE68666 data_bgee_zebrafish_gse68666 <- getSampleProcessedData(bgee, experimentId = "GSE68666") ## ----eval=FALSE--------------------------------------------------------------- # # Examples of data downloading using different filtering combination # # retrieve zebrafish RNA-Seq data for heart (UBERON:0000955) or brain (UBERON:0000948) # data_bgee_zebrafish_filters <- getSampleProcessedData(bgee, anatEntityId = c("UBERON:0000955","UBERON:0000948")) # # retrieve zebrafish RNA-Seq data for embryo (UBERON:0000922) part of the experiment GSE68666 # data_bgee_zebrafish_filters <- getSampleProcessedData(bgee, experimentId = "GSE68666", anatEntityId = "UBERON:0000922") # # retrieve zebrafish RNA-Seq data for head kidney (UBERON:0007132) or swim bladder (UBERON:0006860) from post-juvenile adult stage (UBERON:0000113) # data_bgee_zebrafish_filters <- getSampleProcessedData(bgee, stageId = "UBERON:0000113", anatEntityId = c("UBERON:0007132","UBERON:0006860")) # # retrieve zebrafish RNA-Seq data for brain (UBERON:0000948) and all substructures of brain from post-juvenile adult stage (UBERON:0000113) # data_bgee_zebrafish_filters <- getSampleProcessedData(bgee, stageId = "UBERON:0000113", anatEntityId = "UBERON:0000948", withDescendantAnatEntities = TRUE) ## ----------------------------------------------------------------------------- # use only present calls and fill expression matrix with TPM values gene.expression.zebrafish.tpm <- formatData(bgee, data_bgee_zebrafish_gse68666, callType = "present", stats = "tpm") gene.expression.zebrafish.tpm ## ----eval=FALSE--------------------------------------------------------------- # #create a bgee object to download droplet based data from Gallus gallus # bgee <- Bgee$new(species = "Gallus_gallus", dataType = "sc_droplet_based") # # download cell data for one RNA-seq experiment # cell_data_bgee_gallus_gallus <- getCellProcessedData(bgee, experimentId = "ERP132576") ## ----------------------------------------------------------------------------- # Creating new Bgee class object bgee <- Bgee$new(species = "Danio_rerio", release = "15.2") ## ----------------------------------------------------------------------------- # Loading calls of expression myTopAnatData <- loadTopAnatData(bgee) # Look at the data ## str(myTopAnatData) ## ----eval=FALSE--------------------------------------------------------------- # ## Loading silver and gold expression calls from affymetrix data made on embryonic samples only # ## This is just given as an example, but is not run in this vignette because only few data are returned # bgee <- Bgee$new(species = "Danio_rerio", dataType="affymetrix", release = "15.2") # myTopAnatData <- loadTopAnatData(bgee, stage="UBERON:0000068", confidence="silver") ## ----eval=FALSE--------------------------------------------------------------- # # if (!requireNamespace("BiocManager", quietly=TRUE)) # # install.packages("BiocManager") # # BiocManager::install("biomaRt") # library(biomaRt) # ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="drerio_gene_ensembl", host="mar2016.archive.ensembl.org") # # # get the mapping of Ensembl genes to phenotypes. It will corresponds to the background genes # universe <- getBM(filters=c("phenotype_source"), value=c("ZFIN"), attributes=c("ensembl_gene_id","phenotype_description"), mart=ensembl) # # # select phenotypes related to pectoral fin # phenotypes <- grep("pectoral fin", unique(universe$phenotype_description), value=T) # # # Foreground genes are those with an annotated phenotype related to "pectoral fin" # myGenes <- unique(universe$ensembl_gene_id[universe$phenotype_description %in% phenotypes]) # # # Prepare the gene list vector # geneList <- factor(as.integer(unique(universe$ensembl_gene_id) %in% myGenes)) # names(geneList) <- unique(universe$ensembl_gene_id) # summary(geneList) # # # Prepare the topGO object # myTopAnatObject <- topAnat(myTopAnatData, geneList) ## ----------------------------------------------------------------------------- data(geneList) myTopAnatObject <- topAnat(myTopAnatData, geneList) ## ----------------------------------------------------------------------------- results <- runTest(myTopAnatObject, algorithm = 'weight', statistic = 'fisher') ## ----------------------------------------------------------------------------- # Display results sigificant at a 1% FDR threshold tableOver <- makeTable(myTopAnatData, myTopAnatObject, results, cutoff = 0.01) head(tableOver) ## ----------------------------------------------------------------------------- # In order to retrieve significant genes mapped to the term " paired limb/fin bud" term <- "UBERON:0004357" termStat(myTopAnatObject, term) # 172 genes mapped to this term for Bgee 15.2 genesInTerm(myTopAnatObject, term) # 37 significant genes mapped to this term for Bgee 15.2 annotated <- genesInTerm(myTopAnatObject, term)[["UBERON:0004357"]] annotated[annotated %in% sigGenes(myTopAnatObject)] ## ----eval = FALSE------------------------------------------------------------- # bgee <- Bgee$new(species="Mus_musculus", release = "14.1") # # delete all old .rds files of species Mus musculus # deleteOldData(bgee) ## ----eval = FALSE------------------------------------------------------------- # bgee <- Bgee$new(species="Mus_musculus", release = "14.1") # # delete local SQLite database of species Mus musculus from Bgee 14.1 # deleteLocalData(bgee)