## ----style, eval=TRUE, echo=FALSE, results='asis'------------------------
BiocStyle::latex()


## ----include=FALSE-------------------------------------------------------
library(knitr)
opts_chunk$set(tidy=FALSE)


## ----loadChip------------------------------------------------------------
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")



## ----SessionInfo, echo=FALSE---------------------------------------------
sessionInfo()