## org packages ensids <- c("ENSG00000130720", "ENSG00000103257", "ENSG00000156414", "ENSG00000144644", "ENSG00000159307", "ENSG00000144485") library(org.Hs.eg.db) keytypes(org.Hs.eg.db) columns(org.Hs.eg.db) cols <- c("SYMBOL", "GENENAME") select(org.Hs.eg.db, keys=ensids, columns=cols, keytype="ENSEMBL") ## Annotating DESeq 'result' object library(DESeq2) load("~/Bressanone2014/packages/Morgan2014/inst/script/DESeq-res.rda") library(org.Hs.eg.db) symbols = select(org.Hs.eg.db, rownames(res), "SYMBOL", "ENSEMBL") res$SYMBOL = splitAsList(symbols$SYMBOL, symbols$ENSEMBL)[rownames(res)] res ## brca1 -- symbol to sequence library(org.Hs.eg.db) eid <- select(org.Hs.eg.db, "BRCA1", "ENTREZID", "SYMBOL")[["ENTREZID"]] library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene txid <- select(txdb, eid, "TXNAME", "GENEID")[["TXNAME"]] cds <- cdsBy(txdb, by="tx", use.names=TRUE) brca1cds <- cds[names(cds) %in% txid] library(Gviz) plotTracks(list(GenomeAxisTrack(), AnnotationTrack(brca1cds)) library(BSgenome.Hsapiens.UCSC.hg19) genome <- BSgenome.Hsapiens.UCSC.hg19 tx_seq <- extractTranscriptSeqs(genome, brca1cds) tx_seq ## biomaRt library(biomaRt) head(listMarts(), 3) ## list the marts head(listDatasets(useMart("ensembl")), 3) ## mart datasets ensembl <- ## fully specified mart useMart("ensembl", dataset = "hsapiens_gene_ensembl") head(listFilters(ensembl), 3) ## filters myFilter <- "chromosome_name" substr(filterOptions(myFilter, ensembl), 1, 50) ## return values myValues <- c("21", "22") head(listAttributes(ensembl), 3) ## attributes myAttributes <- c("ensembl_gene_id","chromosome_name") ## assemble and query the mart res <- getBM(attributes = myAttributes, filters = myFilter, values = myValues, mart = ensembl)