pedtools (version 1.1.0)

getSex: Get or set the sex of pedigree members

Description

Functions for retrieving or changing the sex of specified pedigree members.

Usage

getSex(x, ids = NULL, named = FALSE)
setSex(x, ids = NULL, sex)
swapSex(x, ids, verbose = TRUE)

Arguments

x

A ped object or a list of such.

ids

A character vector (or coercible to one) containing ID labels. If NULL, defaults to all members of x.

named

A logical: return a named vector or not.

sex

A numeric vector with entries 1 (= male), 2 (= female) or 0 (= unknown). If ids is NULL, sex must be named with ID labels. If sex is unnamed and shorter than ids it is recycled to length(ids).

verbose

A logical: Verbose output or not.

Value

• getSex(x, ids) returns an integer vector of the same length as ids, with entries 0 (unknown), 1 (male) or 2 (female).

• setSex(x, ids, sex) returns a ped object similar to x, but where the sex of ids is set according to the entries of sex

• swapSex(x, ids) returns a ped object identical to x, but where the sex of ids (and their spouses) are swapped (1 <-> 2).

See Also

ped()

Examples

# NOT RUN {
x = nuclearPed(father = "fa", mother = "mo", children = "ch")

stopifnot(all.equal(
  getSex(x, named = TRUE),
  c(fa = 1, mo = 2, ch = 1)
))

# Make child female
setSex(x, ids = "ch", sex = 2)

# Same, using a named vector
setSex(x, sex = c(ch = 2))

# Swapping sex is sometimes easier,
# since spouses are dealt with automatically
swapSex(x, ids = "fa")

# setting/getting sex in a pedlist
y = list(singleton(1, sex = 2), singleton(2), singleton(3))
sx = getSex(y, named = TRUE)
y2 = setSex(y, sex = sx)

stopifnot(identical(y, y2))

# }