create.pedigree: Create pedigree object

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description

This function can be used to create a pedigree object.

Usage

create.pedigree(ID, Par1, Par2, gener=NULL,sex=NULL,add.ancestors=FALSE,unknown=0)

Arguments

ID	vector of unique IDs identifying individuals
Par1	vector of IDs identifying parent 1 (with animals: sire)
Par2	vector of IDs identifying parent 2 (with animals: dam)
gener	vector identifying the generation. If NULL gener will be 0 for unknown parents and max(gener(Par1),gener(Par2))+1 for generations 1,... .
sex	vector identifying the sex (female=0 and male=1).
add.ancestors	logical. Add ancestors which do not occur in ID to the pedigree.
unknown	value for unknown or missing ancestors.

Details

Missing values for parents in the pedigree should be coded NA. 0 is treaded as unknown, too.

Value

An object of class pedigree. Column gener starts from 0 and pedigree is sorted by generation.

Author(s)

Valentin Wimmer

See Also

plot.pedigree, add.pedigree

Examples

# example with 9 individuals
id <- paste("ID", 1:9, sep="0")
par1 <- paste("ID", c(0,0,0,0,1,1,1,4,7), sep="")
par2 <- paste("ID", c("","","","",2,3,2,5,8), sep="")
gener <- c(0,0,0,0,1,1,1,2,3)

# create pedigree object (using argument gener)
ped <- create.pedigree(id,par1,par2,gener,unknown=c("ID0", "ID"))
ped
plot(ped)

# create pedigree object (without using argument gener)
ped2 <- create.pedigree(id,par1,par2,unknown=c("ID0", "ID"))
ped2

Example output

    ID Par1 Par2 gener
1 ID01    0    0     0
2 ID02    0    0     0
3 ID03    0    0     0
4 ID04    0    0     0
5 ID05  ID1  ID2     1
6 ID06  ID1  ID3     1
7 ID07  ID1  ID2     1
8 ID08  ID4  ID5     2
9 ID09  ID7  ID8     3
IGRAPH 5b952a0 DN-- 9 0 -- 
+ attr: name (v/c), Par1 (v/c), Par2 (v/c), gener (v/n)
+ edges from 5b952a0 (vertex names):
    ID Par1 Par2 gener
1 ID01    0    0     0
2 ID02    0    0     0
3 ID03    0    0     0
4 ID04    0    0     0
5 ID05  ID1  ID2     1
6 ID06  ID1  ID3     1
7 ID07  ID1  ID2     1
8 ID08  ID4  ID5     1
9 ID09  ID7  ID8     1

synbreed documentation built on May 2, 2019, 3:23 a.m.