## ----env, echo=FALSE---------------------------------------------------------- suppressPackageStartupMessages(library("GO.db")) suppressPackageStartupMessages(library("BiocStyle")) suppressPackageStartupMessages(library("rols")) suppressPackageStartupMessages(library("DT")) 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--------------------------------------------------- datatable(as(ol, "data.frame")) ## ----------------------------------------------------------------------------- library("rols") ## ----ol----------------------------------------------------------------------- ol <- Ontologies() ol ## ----------------------------------------------------------------------------- head(olsNamespace(ol)) ol[["go"]] ## ----------------------------------------------------------------------------- go <- Ontology("go") go ## ----------------------------------------------------------------------------- gotrms <- terms(go) ## or terms("go") gotrms gotrms[1:10] gotrms[["GO:0090575"]] ## ----------------------------------------------------------------------------- trm <- term(go, "GO:0090575") termId(trm) termLabel(trm) strwrap(termDesc(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) ## ----tgnquery3---------------------------------------------------------------- (tgnq <- OlsSearch(q = "trans-golgi network", ontology = "GO")) (tgnq <- allRows(tgnq)) ## ----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") CVParam(label = "MS", name ="electrospray ionization") CVParam(label = "MS", name ="ESI") ## using a synonym ## ----si, echo=FALSE----------------------------------------------------------- print(sessionInfo(), locale = FALSE)