makekinship: Create a sparse kinship matrix

In mayoverse/kinship2: Pedigree Functions

Create a sparse kinship matrix

Description

Compute the overall kinship matrix for a collection of families, and store it efficiently.

Usage

makekinship(famid, id, father.id, mother.id, unrelated=0)

Arguments

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.

Details

This command is depricated. The kinship command now can be applied directly to pedigreeList objects.

Value

a sparse kinship matrix of class bdsmatrix

See Also

kinship, makefamid

Examples

# 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)

mayoverse/kinship2 documentation built on July 4, 2023, 1:11 a.m.