kinship2: pedigree.shrink – R documentation

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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.

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.

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

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)

kinship2

Pedigree Functions

v1.8.5

GPL (>= 2)

Authors

Jason Sinnwell [aut, cre], Terry Therneau [aut], Daniel Schaid [ctb], Elizabeth Atkinson [ctb], Carly Mester [ctb]

Initial release

2019-5-31