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## ----style, echo = FALSE, results = 'asis'--------------------------------------------------------
BiocStyle::markdown()
## ----library, message=FALSE-----------------------------------------------------------------------
library(AnnotationHub)
## ----AnnotationHub--------------------------------------------------------------------------------
ah = AnnotationHub()
## ----show-----------------------------------------------------------------------------------------
ah
## ----dataprovider---------------------------------------------------------------------------------
unique(ah$dataprovider)
## ----species--------------------------------------------------------------------------------------
head(unique(ah$species))
## ----rdataclass-----------------------------------------------------------------------------------
head(unique(ah$rdataclass))
## ----dm1------------------------------------------------------------------------------------------
dm <- query(ah, c("ChainFile", "UCSC", "Drosophila melanogaster"))
dm
## ----show2----------------------------------------------------------------------------------------
df <- mcols(dm)
## ----length---------------------------------------------------------------------------------------
length(ah)
## ----subset---------------------------------------------------------------------------------------
ahs <- query(ah, c('inparanoid8', 'ailuropoda'))
ahs
## ----BiocHubsShiny, eval=FALSE--------------------------------------------------------------------
# BiocHubsShiny::BiocHubsShiny()
## ----echo=FALSE,fig.cap="BiocHubsShiny query with terms dataprovider = 'inparanoid' and species = 'ailuropoda'"----
knitr::include_graphics("ailMel1_BiocHubsShiny.png")
## ----dm2------------------------------------------------------------------------------------------
dm
dm["AH15146"]
## ----dm3------------------------------------------------------------------------------------------
dm[["AH15146"]]
## ----show-2---------------------------------------------------------------------------------------
ah
## ----snapshot-------------------------------------------------------------------------------------
snapshotDate(ah)
## ----possibleDates--------------------------------------------------------------------------------
pd <- possibleDates(ah)
pd
## ----setdate, eval=FALSE--------------------------------------------------------------------------
# snapshotDate(ah) <- pd[1]
## ----clusterOptions1, eval=FALSE------------------------------------------------------------------
# library(AnnotationHub)
# hub <- AnnotationHub()
# gr <- hub[["AH50773"]] ## downloaded once
# txdb <- makeTxDbFromGRanges(gr) ## build on the fly
## ----clusterOptions2, eval=FALSE------------------------------------------------------------------
# library(AnnotationDbi) ## if not already loaded
# txdb <- loadDb("/locationToFile/mytxdb.sqlite")
## ----sessionInfo----------------------------------------------------------------------------------
sessionInfo()
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