## ----env, echo=FALSE, message=FALSE------------------------------------------- suppressPackageStartupMessages(library("GO.db")) suppressPackageStartupMessages(library("BiocStyle")) suppressPackageStartupMessages(library("rols")) suppressPackageStartupMessages(library("DT")) suppressMessages(nonto <- length(ol <- Ontologies())) ## ----install, eval=FALSE------------------------------------------------------ # ## try http:// if https:// URLs are not supported # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("rols") ## ----ontTable, echo = FALSE--------------------------------------------------- DT::datatable(as(ol, "data.frame")) ## ----------------------------------------------------------------------------- library("rols") ## ----ol----------------------------------------------------------------------- ol <- Ontologies() ol ## ----------------------------------------------------------------------------- head(olsNamespace(ol)) ol[["bspo"]] ## ----------------------------------------------------------------------------- bspo <- Ontology("bspo") bspo ## ----------------------------------------------------------------------------- bspotrms <- Terms(bspo) ## or Terms("bspo") bspotrms bspotrms[1:10] bspotrms[["BSPO:0000092"]] ## ----------------------------------------------------------------------------- trm <- Term(bspo, "BSPO:0000092") termId(trm) termLabel(trm) ## ----------------------------------------------------------------------------- parents(trm) children(trm) ## ----propex------------------------------------------------------------------- trm <- Term("uberon", "UBERON:0002107") trm p <- Properties(trm) p p[[1]] termLabel(p[[1]]) ## ----echo=FALSE--------------------------------------------------------------- alltgns <- OlsSearch(q = "trans-golgi network") ## ----tgnquery, eval = TRUE---------------------------------------------------- OlsSearch(q = "trans-golgi network") ## ----tgnquery1, eval = TRUE--------------------------------------------------- OlsSearch(q = "trans-golgi network", exact = TRUE) OlsSearch(q = "trans-golgi network", ontology = "GO") OlsSearch(q = "trans-golgi network", ontology = "GO", exact = TRUE) ## ----tgnquery2---------------------------------------------------------------- OlsSearch(q = "trans-golgi network", ontology = "GO", rows = 200) ## ----tgnsear4, echo=FALSE----------------------------------------------------- qry <- OlsSearch(q = "trans-golgi network", exact = TRUE) ## ----tgnquery5---------------------------------------------------------------- qry <- OlsSearch(q = "trans-golgi network", exact = TRUE) (qry <- olsSearch(qry)) ## ----tgnres------------------------------------------------------------------- (qtrms <- as(qry, "Terms")) str(qdrf <- as(qry, "data.frame")) ## ----uterms------------------------------------------------------------------- qtrms <- unique(qtrms) termOntology(qtrms) termNamespace(qtrms) ## ----go.db, message=FALSE----------------------------------------------------- library("GO.db") GOTERM[["GO:0005802"]] ## ----------------------------------------------------------------------------- CVParam(name = "A user param", value = "the value") ## ----------------------------------------------------------------------------- CVParam(label = "MS", accession = "MS:1000073") ## ----si, echo=FALSE----------------------------------------------------------- print(sessionInfo(), locale = FALSE)