ped: Pedigree construction

In magnusdv/pedtools: Creating and Working with Pedigrees and Marker Data

Pedigree construction

Description

This is the basic constructor of ped objects. Utility functions for creating many common pedigree structures are described in ped_basic. See also as.ped() and readPed(), which are more liberal regarding the input format.

Usage

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

singleton(id = 1, sex = 1, famid = "")

singletons(id, sex = 1)

Arguments

id	A vector (coercible to character) of individual ID labels.
fid, mid	Vectors of the same length as id, naming the father and mother of each individual, respectively. Missing parents (i.e., corresponding to founder individuals) may be entered as "0", "" or NA.
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 indicating if the pedigree should be reordered so that all parents precede their children. Default: TRUE.
validate	A logical indicating if a validation of the pedigree structure should be performed. Default: TRUE.
detectLoops	A logical indicating if the presence of loops should be detected. Setting this to FALSE may speed up the processing of large pedigrees. Default: TRUE.
isConnected	A logical indicating if the input is known to be a connected pedigree. Setting this to TRUE speeds up the processing. Default: FALSE.
verbose	A logical.

Details

Each individual must have either both parents specified, or no parents. Missing parents are indicated with entries "0", "" or NA in fid and mid. Note that id,fid,mid are all converted to character vectors before matching to establish the parent connections.

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

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

singletons() creates a list of singletons with the indicated labels and sexes.

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).

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 indicating if the pedigree has unbroken loops, or NA if the status is currently unknown.

• 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.

Author(s)

Magnus Dehli Vigeland

See Also

newPed(), ped_basic, ped_modify, ped_subgroups, relabel()

Examples

# 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
ped(id = 1:4, fid = c(2,0,0,0), mid = c(3,0,0,0), sex = c(1,1,2,1))

# List of singletons
singletons(1:2)

magnusdv/pedtools documentation built on April 25, 2024, 4:25 a.m.