prepare_graph constructs a graph based on mother, father, and offspring links.
Arguments
- .tbl
tibble with columns icol, fcol, mcol. Additional columns will be attributes in the constructed graph.
- icol
column name of column with proband ids.
- fcol
column name of column with father ids.
- mcol
column name of column with mother ids.
- node_attributes
tibble with icol and any additional information, such as sex, lower threshold, and upper threshold. Used to assign attributes to each node in the graph, e.g. lower and upper thresholds to individuals in the graph.
- missingID_patterns
string of missing values in the ID columns. Multiple values can be used, but must be separated by "|". Defaults to "^0$". OBS: "0" is NOT enough, since it relies on regex.
Value
An igraph object. A (directed) graph object based on the links provided in .tbl, potentially with provided attributes stored for each node.
Examples
fam <- data.frame(
id = c("pid", "mom", "dad", "pgf"),
dadcol = c("dad", 0, "pgf", 0),
momcol = c("mom", 0, 0, 0))
thresholds <- data.frame(
id = c("pid", "mom", "dad", "pgf"),
lower = c(-Inf, -Inf, 0.8, 0.7),
upper = c(0.8, 0.8, 0.8, 0.7))
prepare_graph(fam, icol = "id", fcol = "dadcol", mcol = "momcol", node_attributes = thresholds)
#> IGRAPH 63367ba DN-- 4 3 --
#> + attr: name (v/c), lower (v/n), upper (v/n)
#> + edges from 63367ba (vertex names):
#> [1] dad->pid mom->pid pgf->dad