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


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


## ----FileDemo------------------------------------------------------------
library(AnnotationForge)
read.table(system.file("extdata", "hcg110_ID",
                       package="AnnotationDbi"),
           sep = "\t", header = FALSE, as.is = TRUE)[1:5,]


## ----availableDB0s-------------------------------------------------------
  available.db0pkgs()  


## ----GetIntermedDB, eval=FALSE-------------------------------------------
## source("http://bioconductor.org/biocLite.R")
## biocLite("human.db0")


## ----GetOrg.db, eval=FALSE-----------------------------------------------
## biocLite("org.Hs.eg.db")


## ----list Schemas--------------------------------------------------------
available.dbschemas()


## ----SQLForge, tidy=FALSE, results='hide'--------------------------------
hcg110_IDs = system.file("extdata",
                          "hcg110_ID",
                          package="AnnotationDbi")

tmpout = tempdir()

makeDBPackage("HUMANCHIP_DB",
              affy=FALSE,            
              prefix="hcg110",
              fileName=hcg110_IDs,
              baseMapType="gb",
              outputDir = tmpout,
              version="1.0.0",
              manufacturer = "Affymetrix",
              chipName = "Human Cancer G110 Array",
              manufacturerUrl = "http://www.affymetrix.com")


## ----cleanup2, echo=FALSE, results='hide'--------------------------------
file.remove(file.path(tmpout, "hcg110.sqlite"))
file.rename(file.path(tmpout, "hcg110.db"),file.path(tmpout, "foo.db"))


## ----install, eval=FALSE-------------------------------------------------
## install.packages("packageNameAndPath", repos=NULL, type="source")


## ----createSimpleMapping, tidy=FALSE-------------------------------------
library(hgu95av2.db)
hgu95av2NAMESYMBOL <- createSimpleBimap("gene_info",
                                        "gene_name",
                                        "symbol",
                                        hgu95av2.db:::datacache,
                                        "NAMESYMBOL",
                                        "hgu95av2.db")
##What is the mapping we just made?
hgu95av2NAMESYMBOL
##Display the 1st 4 relationships in this new mapping
as.list(hgu95av2NAMESYMBOL)[1:4]


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


