LTFGRS (version 1.0.0)

graph_to_trio: Convert from igraph to trio information

Description

This function converts an igraph object to a trio information format.

Usage

graph_to_trio(
  graph,
  id = "id",
  dadid = "dadid",
  momid = "momid",
  sex = "sex",
  fixParents = TRUE
)

Value

A tibble with trio information.

Arguments

graph

An igraph graph object.

id

Column of proband id. Defaults to id.

dadid

Column of father id. Defaults to dadid.

momid

Column of mother id. Defaults to momid.

sex

Column of sex in igraph attributes. Defaults to sex.

fixParents

Logical. If TRUE, the kinship2's fixParents will be run on the trio information before returning. Defaults to TRUE.

Details

The sex column is required in the igraph attributes. The sex information is used to determine who is the mother and father in the trio.

Examples

if (FALSE) {

family = tribble(
~id, ~momcol, ~dadcol,
"pid", "mom", "dad",
"sib", "mom", "dad",
"mhs", "mom", "dad2",
"phs", "mom2", "dad",
"mom", "mgm", "mgf",
"dad", "pgm", "pgf",
"dad2", "pgm2", "pgf2",
"paunt", "pgm", "pgf",
"pacousin", "paunt", "pauntH",
"hspaunt", "pgm", "newpgf",
"hspacousin", "hspaunt", "hspauntH",
"puncle", "pgm", "pgf",
"pucousin", "puncleW", "puncle",
"maunt", "mgm", "mgf",
"macousin", "maunt", "mauntH",
"hsmuncle", "newmgm", "mgf",
"hsmucousin", "hsmuncleW", "hsmuncle"
)


thrs =  tibble(
  id = family %>% select(1:3) %>% unlist() %>% unique(),
  lower = sample(c(-Inf, 2), size = length(id), replace = TRUE),
  upper = sample(c(2, Inf), size = length(id), replace = TRUE),
 sex = case_when(
   id %in% family$momcol ~ "F",
    id %in% family$dadcol ~ "M",
    TRUE ~ NA)) %>%
  mutate(sex = sapply(sex, function(x) ifelse(is.na(x),
  sample(c("M", "F"), 1), x)))
graph = prepare_graph(.tbl = family,
icol = "id", fcol = "dadcol", mcol = "momcol", node_attributes = thrs)
}