kinship2 (version 1.8.5)

pedigree: Create pedigree structure

Description

Create pedigree structure in the format needed for plotting.

Usage

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

Value

An object of class pedigree or pedigreeList

Containing the following items: famid id findex mindex sex affected status relation

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

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 "" (the empty string) otherwise.

See Also

plot.pedigree, autohint

Examples

data(minnbreast)

bpeds <- with(minnbreast,
    pedigree(id, fatherid, motherid, sex, affected=proband, famid=famid))

## pedigree with id=8
bped.id8 <- bpeds['8']
print(bped.id8)
## to plot:
#plot(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))
## to plot:
#plot(bped.id8)


## the 8th pedigree
bped8 <- bpeds[8]

print(bped8)
## to plot:
#plot(bped8, cex=.5)