convertIBD {KinMixLite}

Convert relationship information to IBD pattern distribution

Description

Construct IBD pattern distribution from one of several alternative representations of multi-person condensed coefficients of identity

Usage

as.IBD(x='sibs', targets=NULL, ped=FALSE) 
convertIBD(x='sibs', targets=NULL, ped=FALSE)

Arguments

x

A string, a vector of length 3 or 9, a list with components pr and patt, or a list with two components, a pedigree and a vector of target id's; see Details

targets

character vector of individual tags

ped

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

Details

Possible formats for the input x are:

1. certain verbal mnemonics; currently one of the following (or an unambiguous partial match): c('sibs','parent-child','half-sibs', 'cousins','half-cousins','second-cousins', 'double-first-cousins', 'quadruple-half-first-cousins', '3cousins-cyclic','3cousins-star','trio')

2. a vector of 3 kappas

3. a vector of 9 Deltas

4. a list with matrix or vector valued component patt, with or without component pr

5. a list with 2 components, the first being a pedigree in the sense of the pedtools package, the second a vector of target id's

6. a 3-column character matrix of individual tags, each row denoting a child/mother/triple - an alternative compact representation of a pedigree

Value

IBD pattern distribution as a list with components pr and patt

Author(s)

Peter Green ([e-mail])

See Also

pedtools, formats

Examples

data(test2data)

IBD<-convertIBD('parent-child')

IBD<-convertIBD(c(0.5,0.5,0.0))