IBD {CrypticIBDcheck}R Documentation

Constructor function for objects of class IBD

Description

Constructor function for objects of class IBD, used as both the input and output of the IBDcheck function. This is not intended to be called by users. Users preparing data for a call to IBDcheck should use the wrapper function new.IBD, which provides basic checks of the input.

Usage

IBD(snp.data, snp.support,subject.support, ibd.study=NULL,
    ibd.ur=NULL,ibd.mz=NULL,ibd.po=NULL,ibd.fs=NULL,ibd.hs=NULL, 
    ibd.co=NULL, ibd.user=NULL, filterparams=NULL,simparams=NULL,call=NULL)

Arguments

snp.data

A snp.matrix object containing the genotypes. Rows correspond to subjects and columns correspond to SNPs.

snp.support

a data frame of SNP information

subject.support

a data frame of subject information

ibd.study

A data frame of estimated IBD coefficients for study subjects. Columns represent estimated probabilities of 0, 1 and 2 alleles IBD. Rows represent pairs of subjects.

ibd.ur

data frame of estimated IBD coefficients for simulated unrelated subjects

ibd.mz

data frame of estimated IBD coefficients for simulated monozygotic twins

ibd.po

data frame of estimated IBD coefficients for simulated parent-offspring subjects

ibd.fs

data frame of estimated IBD coefficients for simulated full sibling subjects

ibd.hs

data frame of estimated IBD coefficients for simulated half sibling subjects

ibd.co

data frame of estimated IBD coefficients for simulated cousins

ibd.user

data frame of estimated IBD coefficients for subjects having a user-defined relationship

filterparams

a list of data filtering options returned by filter.control

simparams

a list of data simulation options returned by sim.control

call

the IBDcheck call that created the ibd.* data frames

Details

Objects of class IBD are both the input and output of the IBDcheck function.

Value

An object of class IBD, which is a list comprised of the function arguments.

Author(s)

Annick Joelle Nembot-Simo, Jinko Graham and Brad McNeney

See Also

IBDcheck


[Package CrypticIBDcheck version 0.3-3 Index]