Familias: ConvertPed – R documentation

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ConvertPed

Converts pedigree data frame to kinship2 pedigree object

Description

A data frame describing a pedigree is converted to a kinship2 pedigree object to be used by say FamiliasPosterior. Typically the input is created using paramlink.

Usage

ConvertPed(ped, persons = NULL)

Arguments

`ped`	A data frame with columns ID, FID (father id), MID (mother id),sex (1=male, 2=female), AFF (not used) possible followed by marker data, two columns for each marker
`persons`	A character vector indicating names of persons in the case ordered as `ped[,1]. In other words, persons[1] corresponds tp ped[1,1] etc.`

Value

`ped`	An object of class pedigree
`datamatrix`	A data frame. One line for each person, one column for each allele.

Author(s)

Thore Egeland <Thore.Egeland@gmail.com>

Examples

persons <- c("AF","mother", "daughter")
ped1=swapSex(nuclearPed(1),3)
locus1=marker(ped1,1,c(1,1),2,c(2,2),3,c(1,2))
ped1=addMarker(ped1,locus1)
# A plot function such as the following can now be used: 
# plot(ped1,marker=1,id.labels=persons,title="ped1") 
ped1=as.data.frame(ped1) 
ConvertPed(ped1,persons)

Familias

Probabilities for Pedigrees Given DNA Data

v2.4

GPL-2

Authors

Petter Mostad, Thore Egeland, Ivar Simonsson

Initial release

2016-02-15