pedigreeIBD {KinMixLite}

Construct IBD pattern distribution from pedigree

Description

Construct IBD pattern distribution from a pedigree and a target list of individuals

Usage

pedigreeIBD(x, targets, cond = TRUE, ped=FALSE, quiet = TRUE, verbose = FALSE)

Arguments

x

A pedigree in pedtools format

targets

Character vector, some or all of the individual identifiers in the pedigree x

cond

should IBD pattern be condensed?

ped

logical, should complete pedigree be added as an attribute to the output, if available?

quiet

should resulting IBD pattern distribution be printed?

verbose

should trace information be printed?

Details

This function computes the multi-person condensed coefficients of identity for an arbitrary set of individuals, in the sparse notation of the IBD pattern distribution of Green and Vigeland (2019).

Value

IBD pattern distribution as a list with components pr and patt

Author(s)

Peter Green ([e-mail])

References

Multi-person condensed coefficients of identity, by Peter J. Green and Magnus Dehli Vigeland, University of Bristol technical report, 2019.

See Also

pedtools, formats

Examples

require(ribd)

id<-c('gf','gm','b1','b2','m','c')
fid<-c(0,0,'gf','gf',0,'b1')
mid<-c(0,0,'gm','gm',0,'m')
sex<-c(1,2,1,1,2,0)   
x<-ped(id,fid,mid,sex)

IBD<-pedigreeIBD(x,c('m','c','b1','b2'))

kappaIBD(x,c('m','c','b1','b2'))