kinship2 (version 1.6.4)

pedigree.shrink: Trim a pedigree to specified bit size with priority placed on trimming uninformative subjects.

Description

Iteratively remove subjects from the pedigree. First remove uninformative subjects, i.e., unavailable (not genotyped) with no available descendants. Next, available terminal subjects with unknown phenotype if both parents available. Last, iteratively shrinks pedigrees by preferentially removing: 1. Subjects with unknown affected status 2. Subjects with unaffected affected status 3. Affected subjects.

Usage

pedigree.shrink(ped, avail, affected=NULL, seed=NULL, maxBits=16)

Arguments

ped

A pedigree object with id, dadid, momid, sex, affected

avail

Vector of availability status (genotyped) 0/1 or TRUE/FALSE

affected

Vector of affected status, 0/1 or TRUE/FALSE. If not given, use the first column of the affected matrix of the pedigree object.

seed

An integer or a saved copy of .Random.seed. This allows simulations to be reproduced by using the same initial seed.

maxBits

Target bit size. Pedigree will be trimmed until bit size is <= maxBits.

Value

An object of class pedigree.shrink which is a list with the following components:

pedObj

pedigree object for the trimmed pedigree

idTrimmed

Vector of IDs of trimmed individuals

idList

List of IDs trimmed each of three stages: unavail, noninform, affect

bitSize

Bit size of the pedigree at each stage of trimming

avail

vector of availability for members of the trimmed pedigree

pedSizeOriginal

The number of individuals in the input pedigree

pedSizeIntermed

The number of individuals in the pedigree after removing unavailable subjects and before beginning the itertive shrinking.

pedSizeFinal

The number of individuals in the final pedigree

seed

The random seed used

Details

If the subject ids are character, make sure none of the characters in the ids is a colon (":"), which is a special character used to concatenate and split subjects within the findUnavailable utility within the pedigree.shrink function.

See Also

findUnavailable, findAvailNonInform, plot.pedigree.shrink

Examples

# NOT RUN {
data(sample.ped)

fam1 <- sample.ped[sample.ped$ped==1,]
ped1 <- pedigree(fam1$id, fam1$father, fam1$mother, fam1$sex,
                 fam1$affected)

shrink1 <- pedigree.shrink(ped=ped1, avail=fam1$avail, maxBits=25)

print(shrink1)
## plot(ped1)
## plot(shrink1, title="Sample Pedigree 1")


fam2 <- sample.ped[sample.ped$ped==2,]
ped2 <- pedigree(fam2$id, fam2$father, fam2$mother, fam2$sex,
                 fam2$affected)

shrink2 <- pedigree.shrink(ped2, avail=fam2$avail)

## plot(ped2)
## plot(shrink2, title="Sample Pedigree 2")
print(shrink2)


# }