## ----style, echo = FALSE, results = 'asis'---------------------------------
BiocStyle::markdown()
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(ebicat38)
names(S4Vectors::mcols(ebicat38))
adinds = grep("autoimmu", ebicat38$MAPPED_TRAIT)
adgr = ebicat38[adinds]
adgr
mcols(adgr)[, c("MAPPED_TRAIT", "MAPPED_TRAIT_URI")]