graph_to_trio: Convert from igraph to trio information

In LTFHPlus: Implementation of LT-FH++

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
)

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.

Value

A tibble with trio information.

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(),
 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)
graph_to_trio(graph)
}

LTFHPlus documentation built on June 8, 2025, 11:47 a.m.