pedigree.shrink: Shrink pedigree object

Description

Shrink pedigree object to specified bit size with priority placed on trimming uninformative subjects. The algorithm is useful for getting a pedigree condensed to a minimally informative size for algorithms or testing that are limited by size of the pedigree.

Usage

pedigree.shrink(ped, avail, affected = NULL, maxBits = 16)
# S3 method for pedigree.shrink
print(x, ...)

Arguments

ped: Pedigree object created by the pedigree function,
avail: vector of binary availability status (0/1), i.e. having data, or sample available
affected: vector of binary affected status (0/1/NA). If NULL, uses first column of the pedigree object affected matrix.
maxBits: Optional, the bit size for which to shrink the pedigree
x: pedigree.shrink object used in method functions
...: optional arguments passed to internal functions

Author

Original by Dan Schaid, updated to kinship2 by Jason Sinnwell

Details

Iteratively remove subjects from the pedigree. The random removal of members was previously controlled by a seed argument, but we remove this, forcing users to control randomness outside the function. 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 individuals (chosen at random if there are multiple of the same status): 1. Subjects with unknown affected status, 2. Subjects with unaffected affected status 3. Affected subjects.

Examples

Run this code

data(sample.ped)
pedAll <- pedigree(sample.ped$id, sample.ped$father, sample.ped$mother,
  sample.ped$sex, affected=cbind(sample.ped$affected, sample.ped$avail),
  famid=sample.ped$ped)
ped1 <- pedAll['1']
pedigree.shrink(ped1, maxBits=12, avail=ped1$affected[,2])