## ----env, echo=FALSE---------------------------------------------------------- suppressPackageStartupMessages(library("dplyr")) 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") ## ----------------------------------------------------------------------------- hpa_data <- allHparData() ## ----echo=FALSE--------------------------------------------------------------- DT::datatable(hpa_data) ## ----------------------------------------------------------------------------- head(normtissue <- hpaNormalTissue()) ## ----message = FALSE---------------------------------------------------------- library("ExperimentHub") eh <- ExperimentHub() query(eh, "hpar") ## ----hpaData------------------------------------------------------------------ names(normtissue) ## Number of genes length(unique(normtissue$Gene)) ## Number of cell types length(unique(normtissue$Cell.type)) ## Number of tissues length(unique(normtissue$Tissue)) ## Number of genes highlighly and reliably expressed in each cell type ## in each tissue. library("dplyr") normtissue |> filter(Reliability == "Approved", Level == "High") |> count(Cell.type, Tissue) |> arrange(desc(n)) |> head() ## ----getHpa------------------------------------------------------------------- id <- "ENSG00000000003" subcell <- hpaSubcellularLoc() rna <- rnaGeneCellLine() ## Compine protein immunohistochemisty data, with the subcellular ## location and RNA expression levels. filter(normtissue, Gene == id) |> full_join(filter(subcell, Gene == id)) |> full_join(filter(rna, Gene == id)) |> head() ## ----getHpa2, eval=FALSE------------------------------------------------------ # browseHPA(id) ## ----rel---------------------------------------------------------------------- getHpaVersion() getHpaDate() getHpaEnsembl() ## ----uc-hpar------------------------------------------------------------------ id <- "ENSG00000001460" filter(subcell, Gene == id) ## ----uc-db-------------------------------------------------------------------- library("org.Hs.eg.db") library("GO.db") ans <- AnnotationDbi::select(org.Hs.eg.db, keys = id, columns = c("ENSEMBL", "GO", "ONTOLOGY"), keytype = "ENSEMBL") ans <- ans[ans$ONTOLOGY == "CC", ] ans sapply(as.list(GOTERM[ans$GO]), slot, "Term") ## ----sessioninfo, echo = FALSE------------------------------------------------ sessionInfo()