## ----style, echo = FALSE, results = 'asis'------------------------------------ suppressPackageStartupMessages({ library(gwascat) }) ## ----getg--------------------------------------------------------------------- library(gwascat) requireNamespace("graph") data(efo.obo.g) efo.obo.g sn = head(graph::nodes(efo.obo.g)) sn ## ----procdef------------------------------------------------------------------ nd = graph::nodeData(efo.obo.g) alldef = sapply(nd, function(x) unlist(x[["def"]])) allnames = sapply(nd, function(x) unlist(x[["name"]])) alld2 = sapply(alldef, function(x) if(is.null(x)) return(" ") else x[1]) mydf = data.frame(id = names(allnames), concept=as.character(allnames), def=unlist(alld2)) ## ----limtab------------------------------------------------------------------- limdf = mydf[ grep("autoimm", mydf$def, ignore.case=TRUE), ] requireNamespace("DT") suppressWarnings({ DT::datatable(limdf, rownames=FALSE, options=list(pageLength=5)) }) ## ----lkg---------------------------------------------------------------------- graph::nodeData(efo.obo.g, "EFO:0000540") ue = graph::ugraph(efo.obo.g) neighISD = graph::adj(ue, "EFO:0000540")[[1]] sapply(graph::nodeData(graph::subGraph(neighISD, efo.obo.g)), "[[", "name") ## ----lkggg-------------------------------------------------------------------- requireNamespace("RBGL") p = RBGL::sp.between( efo.obo.g, "EFO:0000685", "EFO:0000001") sapply(graph::nodeData(graph::subGraph(p[[1]]$path_detail, efo.obo.g)), "[[", "name") ## ----lkef--------------------------------------------------------------------- data(ebicat_2020_04_30) names(S4Vectors::mcols(ebicat_2020_04_30)) adinds = grep("autoimmu", ebicat_2020_04_30$MAPPED_TRAIT) adgr = ebicat_2020_04_30[adinds] adgr S4Vectors::mcols(adgr)[, c("MAPPED_TRAIT", "MAPPED_TRAIT_URI")]