kinship2 (version 1.3.1)

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

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

No further details.

See Also

findUnavailable, findAvailNonInform, plot.pedigree.shrink

Examples

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)