IBDsim: Simulation of Chromosomal Regions Shared by Family Members
Version 0.9-7

Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Kong et. al (2010) ), phased chromosomes are simulated for all pedigree members, either by unconditional gene dropping or conditional on a specified IBD pattern. Additional functions provide summaries and further analysis of the simulated genomes.

AuthorMagnus Dehli Vigeland
Date of publication2017-04-26 17:25:51 UTC
MaintainerMagnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
LicenseGPL (>= 2)
Version0.9-7
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("IBDsim")

Popular man pages

alleleSummary: Allele sharing summary
DecodeMap: Decode recombination map
dominant1: Autosomal dominant pedigree
IBDsim: IBD simulation
oneLocusJacquard: Estimating Jacquard's condensed identity coefficients
twoLocusIBD: Estimating two-locus IBD coefficients
twoLocusJacquard: Estimating two-locus Jacquard coefficients
See all...

All man pages Function index File listing

Man pages

alleleSummary: Allele sharing summary
DecodeMap: Decode recombination map
dominant1: Autosomal dominant pedigree
IBDsim: IBD simulation
oneLocusIBD: Estimating pairwise IBD coefficients
oneLocusJacquard: Estimating Jacquard's condensed identity coefficients
twoLocusIBD: Estimating two-locus IBD coefficients
twoLocusJacquard: Estimating two-locus Jacquard coefficients

Functions

CAFs Source code
DecodeMap Man page
IBDsim Man page Source code
alleleSummary Man page Source code
cm2phys Source code
comb2 Source code
decide_action Source code
distribute.founder.alleles Source code
dominant1 Man page
dropping.order Source code
genedrop Source code
getAlleles Source code
getLocus Source code
ibd.status Source code
jacquard.state Source code
loadMap Source code
meiosis Source code
mergeRuns Source code
obligate.carriers Source code
oneLocusIBD Man page Source code
oneLocusJacquard Man page Source code
pedPaths Source code
phys2cm Source code
pos2allele Source code
prettycat Source code
printSAP Source code
rangeCompl Source code
rangeIntersect Source code
rangeUnion Source code
sample.obligates Source code
sap.finder Source code
sortDouble Source code
summary.ibd Source code
twoLocusIBD Man page Source code
twoLocusJacquard Man page Source code
uniformMap Source code

Files

src
src/IBDsim.c
src/init.c
NAMESPACE
NEWS
data
data/dominant1.rda
data/DecodeMap.rda
data/datalist
R
R/summary.ibd.R
R/IBDsim.R
R/twoLocusIBD.R
R/ped_utils.R
R/meiosis.R
R/alleleSummary.R
R/genedrop.R
R/ibd.runs.R
R/range_utils.R
R/map_utils.R
MD5
DESCRIPTION
man
man/twoLocusJacquard.Rd
man/IBDsim.Rd
man/twoLocusIBD.Rd
man/oneLocusIBD.Rd
man/dominant1.Rd
man/alleleSummary.Rd
man/oneLocusJacquard.Rd
man/DecodeMap.Rd
IBDsim documentation built on May 19, 2017, 12:38 p.m.

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