Find Unrelated subjects

Determine set of maximum number of unrelated available subjects from a Pedigree.

Usage

# S4 method for class 'Ped'
unrelated(obj, avail = NULL)

# S4 method for class 'Pedigree'
unrelated(obj, avail = NULL)

Arguments

obj

A Pedigree or Ped object.

avail

A logical vector with the availability status of the individuals (i.e. FALSE = not available, TRUE = available, NA = unknown).

Value

A vector of the ids of subjects that are unrelated.

Details

Determine set of maximum number of unrelated available subjects from a Pedigree, given vectors id, father, and mother for a Pedigree structure, and status vector of TRUE / FALSE for whether each subject is available (e.g. has DNA).

This is a greedy algorithm that uses the kinship matrix, sequentially removing rows/cols that are non-zero for subjects that have the most number of zero kinship coefficients (greedy by choosing a row of kinship matrix that has the most number of zeros, and then remove any cols and their corresponding rows that are non-zero. To account for ties of the count of zeros for rows, a random choice is made. Hence, running this function multiple times can return different sets of unrelated subjects.

If avail is NULL, it is extracted with its corresponding accessor from the Ped object.

Author

Dan Schaid and Shannon McDonnell updated by Jason Sinnwell

Examples

data(sampleped)
fam1 <- sampleped[sampleped$famid == 1, -16]
ped1 <- Pedigree(fam1)
unrelated(ped1)
#> [1] "1_109" "1_113" "1_129" "1_141"
## some possible vectors
## [1] '110' '113' '133' '109'
## [1] '113' '118' '141' '109'
## [1] '113' '118' '140' '109'
## [1] '110' '113' '116' '109'
## [1] '113' '133' '141' '109'