## ----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()