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mmRmeta/example/DAVID_280819.R
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| #DAVID Web Service 28.08 | |
| #http://bioconductor.org/packages/release/bioc/vignettes/RDAVIDWebService/inst/doc/RDavidWS-vignette.pdf | |
| library("RDAVIDWebService") | |
| david <-DAVIDWebService$new(email="sebastian.lieske@bioinfsys.uni-giessen.de") # does not work | |
| david <- DAVIDWebService(email="sebastian.lieske@bioinfsys.uni-giessen.de", url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/") | |
| geneNames <- rownames(subBRCA) | |
| result <- addList(david, geneNames, idType = "ENSEMBL_GENE_ID", listName = "bimodal", listType = "Gene") | |
| #getIdTypes(david) | |
| #do it again with ENTREZ | |
| ensemblgene <- use_biomaRt(geneNames) | |
| hgnc <- ensemblgene$hgnc_symbol %>% na.omit() %>% .[.!= ""] | |
| entrez <- ensemblgene$entrezgene_id %>% na.omit() | |
| result2 <- addList(david, entrez, idType = "ENTREZ_GENE_ID", listName = "bimodal1", listType = "Gene") | |
| #adds directly to david | |
| termCluster <- getClusterReport(david, type="Term") #terms or genes | |
| getClusterReportFile(david, type="Term", | |
| fileName="termClusterBimodalBRCA.tab") | |
| plot2D(termCluster, 1) | |
| davidGODag<-DAVIDGODag(members(termCluster)[[3]], | |
| pvalueCutoff=0.1, "MF") | |
| plotGOTermGraph(g=goDag(davidGODag), | |
| r=davidGODag, max.nchar=40, node.shape="ellipse") | |
| clust1 <- termCluster@cluster[1] | |
| clust1df <- data.frame(clust1[[1]]$Members) | |
| silver <- use_silvermantest(subBRCA, 2, filter = F, alpha = 0.05, k = 1) | |
| silver2 <- use_silvermantest(subBRCA, 2, filter = F, alpha = 0.05, k = 2) | |
| a <- filter_all(ensemblgene, "X" %in% chromosome_name) |