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

## ----loadPkg----------------------------------------------------------------------------
library(PANTHER.db,quietly=T)

## ----help,eval=FALSE--------------------------------------------------------------------
#  help("PANTHER.db")

## ----show,tidy=TRUE---------------------------------------------------------------------
PANTHER.db

## ----availSpecies-----------------------------------------------------------------------
availablePthOrganisms(PANTHER.db)[1:5,]

## ----setTaxID---------------------------------------------------------------------------
pthOrganisms(PANTHER.db) <- "HUMAN"
PANTHER.db
resetPthOrganisms(PANTHER.db)
PANTHER.db

## ----columns----------------------------------------------------------------------------
columns(PANTHER.db)

## ----keytypes---------------------------------------------------------------------------
keytypes(PANTHER.db)

## ----keys-------------------------------------------------------------------------------
go_ids <- head(keys(PANTHER.db,keytype="GOSLIM_ID"))
go_ids

## ----select-----------------------------------------------------------------------------
cols <- c("FAMILY_ID","CLASS_ID")
res <- select(PANTHER.db, keys=go_ids, columns=cols,keytype="GOSLIM_ID")
head(res)

## ----traverseClassTree------------------------------------------------------------------
term <- "PC00209"
select(PANTHER.db,term, "CLASS_TERM","CLASS_ID")

ancestors <- traverseClassTree(PANTHER.db,term,scope="ANCESTOR")
select(PANTHER.db,ancestors, "CLASS_TERM","CLASS_ID")

parents <- traverseClassTree(PANTHER.db,term,scope="PARENT")
select(PANTHER.db,parents, "CLASS_TERM","CLASS_ID")

children <- traverseClassTree(PANTHER.db,term,scope="CHILD")
select(PANTHER.db,children, "CLASS_TERM","CLASS_ID")

offspring <- traverseClassTree(PANTHER.db,term,scope="OFFSPRING")
select(PANTHER.db,offspring, "CLASS_TERM","CLASS_ID")