## ----figure, fig.cap = "Relationships between Annotation packages", echo = FALSE---- knitr::include_graphics("relationships-between-annotation-packages.png") ## ----columns, message = FALSE, warning = FALSE-------------------------------- library(Homo.sapiens) columns(Homo.sapiens) ## ----keys1, message = FALSE, warning = FALSE---------------------------------- keytypes(Homo.sapiens) ## ----keys2, message = FALSE, warning = FALSE---------------------------------- head(keys(Homo.sapiens, keytype = "ENTREZID")) ## ----select, message = FALSE, warning = FALSE--------------------------------- k <- head(keys(Homo.sapiens, keytype = "ENTREZID"), n = 3) select( Homo.sapiens, keys = k, columns = c("TXNAME", "SYMBOL"), keytype = "ENTREZID" ) ## ----transcripts, message = FALSE, warning = FALSE---------------------------- transcripts(Homo.sapiens, columns = c("TXNAME", "SYMBOL")) ## ----transcriptsBy, message = FALSE, warning = FALSE-------------------------- transcriptsBy(Homo.sapiens, by = "gene", columns = c("TXNAME", "SYMBOL")) ## ----setupColData, message = FALSE, warning = FALSE--------------------------- gd <- list( join1 = c(GO.db = "GOID", org.Hs.eg.db = "GO"), join2 = c( org.Hs.eg.db = "ENTREZID", TxDb.Hsapiens.UCSC.hg19.knownGene = "GENEID" ) ) ## ----makeOrganismPackage, eval = FALSE---------------------------------------- # destination <- tempfile() # dir.create(destination) # makeOrganismPackage( # pkgname = "Homo.sapiens", # graphData = gd, # organism = "Homo sapiens", # version = "1.0.0", # maintainer = "Package Maintainer", # author = "Some Body", # destDir = destination, # license = "Artistic-2.0" # )