CoSeg: An R package for cosegregation analysis and simulating pedigrees

This package contains usefule tools for generating and analyzing pedigrees. Specifically, it contains functions that will generate realistic pedigrees for the USA and China based on historical birth rates and family sizes. It also has functions for analyzing these pedigrees when they include disease information including one based on counting meioses and another based on likelihood ratios.

Author
John Michael O. Ranola and Brian H. Shirts
Date of publication
2016-07-19 07:29:39
Maintainer
John Michael O. Ranola <ranolaj@uw.edu>
License
GPL (>= 2)
Version
0.2

View on R-Forge

Man pages

add.affected.to.tree
Add affection status to a given tree
BRCA1frequencies.df
BRCA1 cancer incidence data frame
BRCA2frequencies.df
BRCA2 cancer incidence data frame
calculate.likelihood.ratio
A function to calculate the likelihood ratio
ChinaDemographics.df
Chinese Demographics Data Frame
CoSeg-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("CoSeg")}
LSfrequencies.df
Lynch Syndrome cancer incidence data frame
make.affected.trees
Make affected trees
make.tree
Make a tree
plot.ped
Plots a tree/pedigree
USDemographics.df
United States Demographics Data Frame

Files in this package

CoSeg/DESCRIPTION
CoSeg/NAMESPACE
CoSeg/R
CoSeg/R/CoSeg-internal.R
CoSeg/R/add.affected.to.tree.R
CoSeg/R/make.affected.trees.R
CoSeg/R/make.tree.R
CoSeg/R/plot.ped.R
CoSeg/R/rank.members.R
CoSeg/build
CoSeg/build/partial.rdb
CoSeg/data
CoSeg/data/BRCA1frequencies.df.rda
CoSeg/data/BRCA2frequencies.df.rda
CoSeg/data/ChinaDemographics.df.rda
CoSeg/data/LSfrequencies.df.rda
CoSeg/data/USDemographics.df.rda
CoSeg/man
CoSeg/man/BRCA1frequencies.df.Rd
CoSeg/man/BRCA2frequencies.df.Rd
CoSeg/man/ChinaDemographics.df.Rd
CoSeg/man/CoSeg-package.Rd
CoSeg/man/LSfrequencies.df.Rd
CoSeg/man/USDemographics.df.Rd
CoSeg/man/add.affected.to.tree.Rd
CoSeg/man/calculate.likelihood.ratio.Rd
CoSeg/man/make.affected.trees.Rd
CoSeg/man/make.tree.Rd
CoSeg/man/plot.ped.Rd
CoSeg/src
CoSeg/src/LikelihoodRatio.f90
CoSeg/src/constants.mod
CoSeg/src/rprint.mod