Create a pedigree or pedigreeList object
pedigree(id, dadid, momid, sex, affected, status, relation, famid, missid)# S3 method for pedigreeList
[(x, ..., drop = FALSE)
# S3 method for pedigree
[(x, ..., drop = FALSE)
# S3 method for pedigree
print(x, ...)
# S3 method for pedigreeList
print(x, ...)
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)
Identification variable for individual
Identification variable for father. Founders' parents should be coded to NA, or another value specified by missid.
Identification variable for mother. Founders' parents should be coded to NA, or another value specified by missid.
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.
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.
Censor/Vital status (0="censored", 1="dead")
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.
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.
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.
pedigree object in print and subset methods
optional arguments passed to internal functions
logical, used in subset function for dropping dimensionanlity
Terry Therneau
kinship, plot.pedigree, autohint