pedtools (version 1.1.0)

ped: Pedigree construction

Description

This is the basic constructor of ped objects. Utility functions for creating many common pedigree structures are described in ped_basic.

Usage

ped(
  id,
  fid,
  mid,
  sex,
  famid = "",
  reorder = TRUE,
  validate = TRUE,
  isConnected = FALSE,
  verbose = FALSE
)
singleton(id = 1, sex = 1, famid = "")

Arguments

id

a vector (numeric or character) of individual ID labels.

fid

a vector of the same length as id, containing the labels of the fathers. In other words fid[i] is the father of id[i], or 0 if id[i] is a founder.

mid

a vector of the same length as id, containing the labels of the mothers. In other words mid[i] is the mother of id[i], or 0 if id[i] is a founder.

sex

a numeric of the same length as id, describing the genders of the individuals (in the same order as id.) Each entry must be either 1 (=male), 2 (=female) or 0 (=unknown).

famid

a character string. Default: An empty string.

reorder

a logical. If TRUE, the pedigree is reordered so that all parents precede their children.

validate

a logical. If TRUE, validatePed() is run before returning the pedigree.

isConnected

a logical, by default FALSE. If it is known that the input is connected, setting this to TRUE speeds up the processing.

verbose

a logical.

Value

A ped object, which is essentially a list with the following entries:

• ID : A character vector of ID labels. Unless the pedigree is reordered during creation, this equals as.character(id)

• FIDX : An integer vector with paternal indices: For each \(j = 1,2,...\), the entry FIDX[j] is 0 if ID[j] has no father within the pedigree; otherwise ID[FIDX[j]] is the father of ID[j].

• MIDX : An integer vector with maternal indices: For each \(j = 1,2,...\), the entry MIDX[j] is 0 if ID[j] has no mother within the pedigree; otherwise ID[MIDX[j]] is the mother of ID[j].

• SEX : An integer vector with gender codes. Unless the pedigree is reordered, this equals as.integer(sex).

• FAMID : The family ID.

• UNBROKEN_LOOPS : A logical: TRUE if the pedigree is inbred.

• LOOP_BREAKERS : A matrix with loop breaker ID's in the first column and their duplicates in the second column. All entries refer to the internal IDs. This is usually set by breakLoops().

• FOUNDER_INBREEDING : A list of two potential entries, "autosomal" and "x"; both numeric vectors with the same length as founders(x). FOUNDER_INBREEDING is always NULL when a new ped is created. See founderInbreeding().

• MARKERS : A list of marker objects, or NULL.

Details

A singleton is a special ped object whose pedigree contains 1 individual. The class attribute of a singleton is c('singleton', 'ped').

Selfing, i.e. the presence of pedigree members whose father and mother are the same individual, is allowed in ped objects. Any such "self-fertilizing" parent must have undecided sex (sex = 0).

If the pedigree is disconnected, it is split into its connected components and returned as a list of ped objects.

See Also

ped_basic, ped_modify, ped_subgroups, relabel()

Examples

# NOT RUN {
# Trio
x = ped(id = 1:3, fid = c(0,0,1), mid = c(0,0,2), sex = c(1,2,1))

# Female singleton
y = singleton('NN', sex = 2)

# Selfing
z = ped(id = 1:2, fid = 0:1, mid = 0:1, sex = 0:1)
stopifnot(hasSelfing(z))

# Disconnected pedigree: Trio + singleton
w = ped(id = 1:4, fid = c(2,0,0,0), mid = c(3,0,0,0), sex = c(1,1,2,1))
stopifnot(is.pedList(w), length(w) == 2)

# }