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.
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)
}