pedParts | R Documentation |
Utility functions for 'linkdat' objects, mainly for extracting various pedigree information.
offspring(x, id, original.id = TRUE) spouses(x, id, original.id = TRUE) related.pairs( x, relation = c("parents", "siblings", "grandparents", "nephews_nieces", "cousins", "spouses", "unrelated"), available = F, interfam = c("none", "founders", "all"), ... ) unrelated(x, id, original.id = TRUE) leaves(x) parents(x, id, original.id = TRUE) grandparents(x, id, degree = 2, original.id = TRUE) siblings(x, id, half = NA, original.id = TRUE) cousins(x, id, degree = 1, removal = 0, half = NA, original.id = TRUE) nephews_nieces(x, id, removal = 1, half = NA, original.id = TRUE) ancestors(x, id) descendants(x, id, original.id = TRUE)
x |
a |
id |
a numerical ID label. |
original.id |
a logical indicating whether 'id' refers to the original ID label or the internal labeling. |
relation |
one of the words (possibly truncated) |
available |
a logical, if TRUE only pairs of available individuals are returned. |
interfam |
one of the words (possibly truncated) |
... |
further parameters |
degree |
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 included. |
removal |
a non-negative integer |
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.
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))
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