/usr/lib/R/site-library/AnnotationDbi/doc/IntroToAnnotationPackages.R is in r-bioc-annotationdbi 1.26.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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")
## ----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()
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