## ----env, echo=FALSE---------------------------------------------------------- suppressPackageStartupMessages(library("BiocStyle")) suppressPackageStartupMessages(library("org.Hs.eg.db")) suppressPackageStartupMessages(library("GO.db")) ## ----install, eval = FALSE---------------------------------------------------- # ## install BiocManager only one # install.packages("BiocManager") # ## install hpar # BiocManager::install("hpar") ## ----load--------------------------------------------------------------------- library("hpar") ## ----hpaData------------------------------------------------------------------ data(hpaNormalTissue) dim(hpaNormalTissue) names(hpaNormalTissue) ## Number of genes length(unique(hpaNormalTissue$Gene)) ## Number of cell types length(unique(hpaNormalTissue$Cell.type)) head(levels(hpaNormalTissue$Cell.type)) ## Number of tissues length(unique(hpaNormalTissue$Tissue)) head(levels(hpaNormalTissue$Tissue)) ## ----getHpa------------------------------------------------------------------- id <- "ENSG00000000003" head(getHpa(id, hpadata = "hpaNormalTissue")) getHpa(id, hpadata = "hpaSubcellularLoc") head(getHpa(id, hpadata = "rnaGeneCellLine")) ## ----getHpa2, eval=FALSE------------------------------------------------------ # getHpa(id, type = "details") ## ----opts--------------------------------------------------------------------- getHparOptions() setHparOptions(hpadata = "hpaSubcellularLoc") getHparOptions() getHpa(id) ## ----rel---------------------------------------------------------------------- getHpaVersion() getHpaDate() getHpaEnsembl() ## ----uc-hpar------------------------------------------------------------------ id <- "ENSG00000001460" getHpa(id, "hpaSubcellularLoc") ## ----uc-db-------------------------------------------------------------------- library("org.Hs.eg.db") library("GO.db") ans <- select(org.Hs.eg.db, keys = id, columns = c("ENSEMBL", "GO", "ONTOLOGY"), keytype = "ENSEMBL") ans <- ans[ans$ONTOLOGY == "CC", ] ans sapply(as.list(GOTERM[ans$GO]), slot, "Term") ## ----sessioninfo, echo = FALSE------------------------------------------------ sessionInfo()