makekinship | R Documentation |
Compute the overall kinship matrix for a collection of families, and store it efficiently.
makekinship(famid, id, father.id, mother.id, unrelated=0)
famid |
a vector of family identifiers |
id |
a vector of unique subject identifiers |
father.id |
for each subject, the identifier of their biolgical father |
mother.id |
for each subject, the identifier of thier biological mother |
unrelated |
subjects with this family id are considered to be unrelated singletons, i.e., not related to each other or to anyone else. |
This command is depricated. The kinship command now can be applied directly to pedigreeList objects.
a sparse kinship matrix of class bdsmatrix
kinship
, makefamid
# Data set from a large family study of breast cancer # there are 26050 subjects in the file, from 426 families ## Not run: > table(cdata$sex) F M 12699 13351 > length(unique(cdata$famid)) [1] 426 > kin1 <- makekinship(cdata$famid, cdata$gid, cdata$dadid, cdata$momid) > dim(kin1) [1] 26050 26050 > class(kin1) [1] "bdsmatrix" # The next line shows that few of the elements of the full matrix are >0 > length(kin1@blocks)/ prod(dim(kin1)) [1] 0.00164925 # kinship matrix for the females only > femid <- cdata$gid[cdata$sex=='F'] > femindex <- !is.na(match(dimnames(kin1)[[1]], femid)) > kin2 <- kin1[femindex, femindex] # # Note that "femindex <- match(femid, dimnames(kin1)[[1]])" is wrong, since # then kin1[femindex, femindex] might improperly reorder the rows/cols # (if families were not contiguous in cdata). # However sort(match(femid, dimnames(kin1)[[1]])) would be okay. ## End(Not run)
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