LTFHPlus (version 2.2.0)

prepare_graph: Construct graph from register information

Description

prepare_graph constructs a graph based on mother, father, and offspring links.

Usage

prepare_graph(
  .tbl,
  icol,
  fcol,
  mcol,
  node_attributes = NA,
  missingID_patterns = "^0$"
)

Value

An igraph object. A (directed) graph object based on the links provided in .tbl, potentially with provided attributes stored for each node.

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.

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)