graph_to_trio {LTFGRS} | R Documentation |
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(),
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)
}
[Package LTFGRS version 1.0.0 Index]