kinship2: Pedigree Functions

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Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.

Author
Terry M Therneau [aut], Schaid Daniel [ctb], Jason Sinnwell [aut, cre], Elizabeth Atkinson [ctb]
Date of publication
2015-08-03 21:10:46
Maintainer
Jason Sinnwell <sinnwell.jason@mayo.edu>
License
GPL (>= 2)
Version
1.6.4
URLs

View on CRAN

Man pages

align.pedigree
Generate plotting information for a pedigree
autohint
Align a pedigree to print well
bitSize
Calculate pedigree bitsize, defined as 2 * # NonFounders - #...
familycheck
Error check for a family classification
findAvailAffected
Find a single person to trim from a pedigree whose is...
findAvailNonInform
Find subjects from a pedigree who are available and...
findUnavailable
Find unavailable subjects in a pedigree
ibdMatrix
Create an IBD matrix
kindepth
Compute the depth of each subject in a pedigree
kinship
Compute a kinship matrix
makefamid
Construct a family id from pedigree information
makekinship
Create a sparse kinship matrix
minnbreast
Minnesota Breast Cancer Study
pedigree
Create pedigree structure
pedigree.legend
Plot a pedigree legend
pedigree.shrink
Trim a pedigree to specified bit size with priority placed on...
pedigree.unrelated
Determine set of maximum number of unrelated available...
plot.pedigree
plot pedigrees
plot.pedigree.shrink
plot pedigree.shrink object that is a shrunk pedigree object
printBanner
Print a nice banner
sample.ped
Two example pedigrees
testped1
testped1

Files in this package

kinship2
kinship2/inst
kinship2/inst/COPYRIGHT
kinship2/inst/NEWS.Rd
kinship2/inst/doc
kinship2/inst/doc/pedigree.snw
kinship2/inst/doc/pedigree.pdf
kinship2/inst/doc/pedigree.R
kinship2/inst/GPL2.txt
kinship2/tests
kinship2/tests/test.pedigree.trim.R
kinship2/tests/kin1.Rout.save
kinship2/tests/test.pedigree.legend.R
kinship2/tests/ped3.txt
kinship2/tests/subscript.Rout.save
kinship2/tests/makefam.Rout.save
kinship2/tests/test.kinX.Rout.save
kinship2/tests/sampleped1.pdf
kinship2/tests/ped2.pdf
kinship2/tests/ped1.pdf
kinship2/tests/kin1.R
kinship2/tests/monozygote.R
kinship2/tests/failure.R
kinship2/tests/twin.Rout.save
kinship2/tests/ped27_71.txt
kinship2/tests/failure.Rout.save
kinship2/tests/makefam.R
kinship2/tests/test.kinX.R
kinship2/tests/test.pedigree.legend.Rout.save
kinship2/tests/test.pedigree.trim.Rout.save
kinship2/tests/subscript.R
kinship2/tests/test.pedigree.shrink.R
kinship2/tests/monozygote.Rout.save
kinship2/tests/test.pedigree.shrink.Rout.save
kinship2/tests/test.pedigree.unrelated.R
kinship2/tests/twin.R
kinship2/tests/test.pedigree.unrelated.Rout.save
kinship2/NAMESPACE
kinship2/noweb
kinship2/noweb/Makefile
kinship2/noweb/all.toc
kinship2/noweb/all.log
kinship2/noweb/plot.Rnw
kinship2/noweb/noweb.sty
kinship2/noweb/pedigree.R
kinship2/noweb/pedigree.shrink.Rnw
kinship2/noweb/kinship.Rnw
kinship2/noweb/all.tex
kinship2/noweb/MAINTAIN.steps
kinship2/noweb/figure
kinship2/noweb/figure/pdraw3.s
kinship2/noweb/figure/pdraw1.s
kinship2/noweb/figure/pdraw2.s
kinship2/noweb/all.aux
kinship2/noweb/pedigree.Rnw
kinship2/noweb/checks.Rnw
kinship2/noweb/align2.Rnw
kinship2/noweb/kinship.R
kinship2/noweb/noweb.R
kinship2/noweb/align.Rnw
kinship2/noweb/all.nw
kinship2/data
kinship2/data/sample.ped.tab.gz
kinship2/data/testped1.tab.gz
kinship2/data/minnbreast.rda
kinship2/R
kinship2/R/findUnavailable.R
kinship2/R/alignped1.R
kinship2/R/print.pedigree.R
kinship2/R/as.data.frame.pedigree.R
kinship2/R/makefamid.R
kinship2/R/alignped2.R
kinship2/R/alignped4.R
kinship2/R/besthint.R
kinship2/R/familycheck.R
kinship2/R/pedigree.R
kinship2/R/pedigree.unrelated.R
kinship2/R/pedigree.trim.R
kinship2/R/findAvailNonInform.R
kinship2/R/check.hint.R
kinship2/R/printBanner.R
kinship2/R/fscore.pedigree.R
kinship2/R/makekinship.R
kinship2/R/descendant.pedigree.R
kinship2/R/pedigree.legend.R
kinship2/R/findAvailAffected.R
kinship2/R/plot.pedigree.R
kinship2/R/alignped3.R
kinship2/R/kindepth.R
kinship2/R/pedigree.shrink.minor.R
kinship2/R/plot.pedigree.shrink.R
kinship2/R/bitSize.R
kinship2/R/align.pedigree.R
kinship2/R/ped2df.R
kinship2/R/kinship.R
kinship2/R/autohint.R
kinship2/R/ibdMatrix.R
kinship2/R/print.pedigree.shrink.R
kinship2/R/pedigree.shrink.R
kinship2/vignettes
kinship2/vignettes/pedigree.snw
kinship2/MD5
kinship2/build
kinship2/build/vignette.rds
kinship2/DESCRIPTION
kinship2/man
kinship2/man/ibdMatrix.Rd
kinship2/man/findAvailAffected.Rd
kinship2/man/align.pedigree.Rd
kinship2/man/findUnavailable.Rd
kinship2/man/bitSize.Rd
kinship2/man/kindepth.Rd
kinship2/man/testped1.Rd
kinship2/man/pedigree.legend.Rd
kinship2/man/findAvailNonInform.Rd
kinship2/man/kinship.Rd
kinship2/man/pedigree.Rd
kinship2/man/familycheck.Rd
kinship2/man/pedigree.shrink.Rd
kinship2/man/makefamid.Rd
kinship2/man/plot.pedigree.Rd
kinship2/man/printBanner.Rd
kinship2/man/makekinship.Rd
kinship2/man/minnbreast.Rd
kinship2/man/plot.pedigree.shrink.Rd
kinship2/man/autohint.Rd
kinship2/man/sample.ped.Rd
kinship2/man/pedigree.unrelated.Rd