Create a sparse kinship matrix
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
# 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.