pedigree: Create a pedigree or pedigreeList object

In kinship2: Pedigree Functions

Create a pedigree or pedigreeList object

Description

Create a pedigree or pedigreeList object

Usage

pedigree(id, dadid, momid, sex, affected, status, relation, famid, missid)

## S3 method for class 'pedigreeList'
x[..., drop = FALSE]

## S3 method for class 'pedigree'
x[..., drop = FALSE]

## S3 method for class 'pedigree'
print(x, ...)

## S3 method for class 'pedigreeList'
print(x, ...)

Arguments

id	Identification variable for individual
dadid	Identification variable for father. Founders' parents should be coded to NA, or another value specified by missid.
momid	Identification variable for mother. Founders' parents should be coded to NA, or another value specified by missid.
sex	Gender of individual noted in ‘id’. Either character ("male","female", "unknown","terminated") or numeric (1="male", 2="female", 3="unknown", 4="terminated") data is allowed. For character data the string may be truncated, and of arbitrary case.
affected	A variable indicating affection status. A multi-column matrix can be used to give the status with respect to multiple traits. Logical, factor, and integer types are converted to 0/1 representing unaffected and affected, respectively. NAs are considered missing.
status	Censor/Vital status (0="censored", 1="dead")
relation	A matrix with 3 required columns (id1, id2, code) specifying special relationship between pairs of individuals. Codes: 1=Monozygotic twin, 2=Dizygotic twin, 3=Twin of unknown zygosity, 4=Spouse. (The last is necessary in order to place a marriage with no children into the plot.) If famid is given in the call to create pedigrees, then famid needs to be in the last column of the relation matrix. Note for tuples of >= 3 with a mixture of zygosities, the plotting is limited to showing pairwise zygosity of adjacent subjects, so it is only necessary to specify the pairwise zygosity, in the order the subjects are given or appear on the plot.
famid	An optional vector of family identifiers. If it is present the result will contain individual pedigrees for each family in the set, which can be extacted using subscripts. Individuals need to have a unique id within family.
missid	The founders are those with no father or mother in the pedigree. The dadid and momid values for these subjects will either be NA or the value of this variable. The default for missid is 0 if the id variable is numeric, and "" (empty string) otherwise.
x	pedigree object in print and subset methods
...	optional arguments passed to internal functions
drop	logical, used in subset function for dropping dimensionanlity

Value

An object of class pedigree or pedigreeList Containing the following items: famid id findex mindex sex affected status relation @examples data(minnbreast) bpeds <- with(minnbreast, pedigree(id, fatherid, motherid, sex, affected=proband, famid=famid)) bped.id8 <- bpeds['8'] print(bped.id8) ## show this pedigree with mixed zygosity quadruplets rel8 <- data.frame(id1=c(137,138,139), id2=c(138,139,140), code=c(1,2,2)) bped.id8 <- with(minnbreast[minnbreast$famid==8,], pedigree(id, fatherid, motherid, sex, affected=proband, relation=rel8)) print(bped.id8)

Author(s)

Terry Therneau

See Also

kinship, plot.pedigree, autohint

kinship2 documentation built on May 29, 2024, 11:14 a.m.