paramlink (version 1.1-0)

linkdat.utils: linkdat utilities

Description

Utility functions for 'linkdat' objects, mainly for extracting various pedigree information.

Usage

ancestors(x, id)
descendants(x, id, original.id=TRUE)
cousins(x, id, degree=1, removal=0, half=NA, original.id=TRUE)
grandparents(x, id, degree=2, original.id=TRUE)
nephews_nieces(x, id, removal=1, half=NA, original.id=TRUE)
parents(x, id, original.id=TRUE)
offspring(x, id, original.id=TRUE)
siblings(x, id, half=NA, original.id=TRUE)
spouses(x, id, original.id=TRUE)
unrelated(x, id, original.id=TRUE)
related.pairs(x, relation=c('parents', 'siblings', 'grandparents', 'nephews_nieces', 
              'cousins', 'spouses', 'unrelated'), available=F, original.id=T, 
              interfam=c("none", "founders", "all"), ...)
leaves(x)
# S3 method for linkdat
all.equal(target, current, ...)

Arguments

x

a linkdat object. In related.pairs possibly a list of linkdat objects.

id

a numerical ID label.

original.id

a logical indicating whether 'id' refers to the original ID label or the internal labeling.

degree

a non-negative integer.

removal

a non-negative integer

half

a logical or NA. If TRUE (resp FALSE), only half (resp. full) siblings/cousins/nephews/nieces are returned. If NA, both categories are inclucded.

relation

one of the words (possibly truncated) parents, siblings, grandparents, nephews_nieces, cousins, spouses, unrelated.

interfam

one of the words (possibly truncated) none, founders or all, specifying which interfamiliar pairs should be included as unrelated in the case where x is a list of several pedigrees. If none, only intrafamiliar pairs are considered; if founders all interfamiliar pairs of (available) founders are included; if all, all interfamiliar (available) pairs are included.

available

a logical, if TRUE only pairs of available individuals are returned.

target, current

the linkdat objects to be compared.

...

Not used.

Value

For ancestors(x,id), a vector containing the ID's of all ancestors of the individual id. For descendants(x,id), a vector containing the ID's of all descendants (i.e. children, grandchildren, a.s.o.) of individual id.

The functions cousins, grandparents, nephews_nieces, offspring, parents, siblings, spouses, unrelated, each returns an integer vector containing the ID's of all pedigree members having the specified relationship with id.

For related.pairs a matrix with two columns. Each row gives of a pair of pedigree members with the specified relation. If the input is a list of multiple pedigrees, the matrix entries are characters of the form "X-Y" where X is the family ID and Y the individual ID of the person.

For leaves, a vector of IDs containing all pedigree members without children.

Examples

# NOT RUN {
p = cbind(ID=2:9, FID=c(0,0,2,0,4,4,0,2), MID=c(0,0,3,0,5,5,0,8), 
        SEX=c(1,2,1,2,1,2,2,2), AFF=c(2,1,2,1,2,1,1,2))
x = linkdat(p)
stopifnot(setequal(spouses(x, 2), c(3,8)), 
          setequal(offspring(x, 2), c(4,9)), 
          setequal(descendants(x, 2), c(4,6,7,9)), 
          setequal(leaves(x), c(6,7,9)))

# Creating a loop and detecting it with 'pedigreeLoops' 
# (note that we get two loops, one for each inbred child):
loopx = addOffspring(x, father=4, mother=9, noffs=2)
lps = pedigreeLoops(loopx)
stopifnot(lps[[1]]$top == 2, setequal(sapply(lps, '[[', 'bottom'), 10:11))

# We add genotypes for a single SNP marker and compute a LOD score under a dominant model.
loopx = setMarkers(loopx, cbind(1,c(2,1,2,1,2,1,1,2,1,1)))
loopx = setModel(loopx, 1)

# Loops are automatically broken in lod():
LOD1 = lod(loopx, theta=0.1)
stopifnot(round(LOD1, 3) == 1.746)

# Or we can break the loop manually before computing the LOD:
loopfree = breakLoops(loopx, loop_breaker=4)
LOD2 = lod(loopfree, theta=0.1)
stopifnot(all.equal(loopx, tieLoops(loopfree)))
stopifnot(all.equal(LOD1, LOD2))
# }