## ----style, eval=TRUE, echo=FALSE, results='asis'-------------------------- BiocStyle::latex() ## ----include=FALSE--------------------------------------------------------- library(knitr) opts_chunk$set(tidy=FALSE) ## ----loadChip-------------------------------------------------------------- suppressPackageStartupMessages({ library(hgu95av2.db) }) ## ----listContents---------------------------------------------------------- ls("package:hgu95av2.db") ## ----show------------------------------------------------------------------ hgu95av2.db ## ----columns--------------------------------------------------------------- columns(hgu95av2.db) ## ----help, eval=FALSE------------------------------------------------------ # help("SYMBOL") ## ----keytypes-------------------------------------------------------------- keytypes(hgu95av2.db) ## ----keys------------------------------------------------------------------ head(keys(hgu95av2.db, keytype="SYMBOL")) ## ----selectChip------------------------------------------------------------ #1st get some example keys k <- head(keys(hgu95av2.db,keytype="PROBEID")) # then call select select(hgu95av2.db, keys=k, columns=c("SYMBOL","GENENAME"), keytype="PROBEID") ## ----mapIdsChip------------------------------------------------------------ #1st get some example keys k <- head(keys(hgu95av2.db,keytype="PROBEID")) # then call mapIds mapIds(hgu95av2.db, keys=k, column=c("GENENAME"), keytype="PROBEID") ## ----selectOrg1------------------------------------------------------------ library(org.Hs.eg.db) columns(org.Hs.eg.db) ## ----selectOrg2, eval=FALSE------------------------------------------------ # help("SYMBOL") ## for explanation of these columns and keytypes values ## ----selectOrg3------------------------------------------------------------ keytypes(org.Hs.eg.db) uniKeys <- head(keys(org.Hs.eg.db, keytype="UNIPROT")) cols <- c("SYMBOL", "PATH") select(org.Hs.eg.db, keys=uniKeys, columns=cols, keytype="UNIPROT") ## ----selectData------------------------------------------------------------ load(system.file("extdata", "resultTable.Rda", package="AnnotationDbi")) head(resultTable) ## ----selectOrgData--------------------------------------------------------- annots <- select(org.Hs.eg.db, keys=rownames(resultTable), columns=c("SYMBOL","GENENAME"), keytype="ENTREZID") resultTable <- merge(resultTable, annots, by.x=0, by.y="ENTREZID") head(resultTable) ## ----selectGO-------------------------------------------------------------- library(GO.db) GOIDs <- c("GO:0042254","GO:0044183") select(GO.db, keys=GOIDs, columns="DEFINITION", keytype="GOID") ## ----selectTxDb------------------------------------------------------------ library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene txdb columns(txdb) keytypes(txdb) keys <- head(keys(txdb, keytype="GENEID")) cols <- c("TXID", "TXSTART") select(txdb, keys=keys, columns=cols, keytype="GENEID") ## ----selectEnsDb----------------------------------------------------------- library(EnsDb.Hsapiens.v75) edb <- EnsDb.Hsapiens.v75 edb ## List all columns columns(edb) ## List all keytypes keytypes(edb) ## Get the first keys <- head(keys(edb, keytype="GENEID")) ## Get the data select(edb, keys=keys, columns=c("TXID", "TXSEQSTART", "TXBIOTYPE"), keytype="GENEID") ## ----selectEnsDb.Y--------------------------------------------------------- ## Retrieve all gene IDs of all lincRNAs encoded on chromosome Y linkY <- keys(edb, filter=list(GeneBiotypeFilter("lincRNA"), SeqNameFilter("Y"))) length(linkY) ## We get now all transcripts for these genes. txs <- select(edb, keys=linkY, columns=c("TXID", "TXSEQSTART", "TXBIOTYPE"), keytype="GENEID") nrow(txs) ## Alternatively, we could specify/pass the filters with the keys argument. txs <- select(edb, keys=list(GeneBiotypeFilter("lincRNA"), SeqNameFilter("Y")), columns=c("TXID", "TXSEQSTART", "TXBIOTYPE")) nrow(txs) ## ----SessionInfo, echo=FALSE----------------------------------------------- sessionInfo()