model.matrix: Model matrix for individuals with and without records

In GeneticsPed: Pedigree and genetic relationship functions

Description

model.matrix for pedigree creates design matrix (Z) for individuals with and without records. Used mainly for educational purposes.

Usage

## S3 method for class 'Pedigree'
model.matrix(object, y, id, left=TRUE, names=TRUE,
                                ...)

Arguments

object	Pedigree
names	logical, should returned matrix have row/colnames; this can be used to get leaner matrix
y	numeric, vector of (phenotypic) records
id	vector of subjects for y
left	logical, bind columns of individuals without records to left (left=TRUE) or right (left=FALSE) side of Z
...	arguments passed to model.matrix

Value

A model matrix of n * q dimension, where n is number of records in y and q is number of subjects in the pedigree

Author(s)

Gregor Gorjanc

See Also

Pedigree, relationshipAdditive, inverseAdditive and model.matrix

Examples

  data(Mrode3.1)
  (x <- Pedigree(x=Mrode3.1, subject="calf", ascendant=c("sire", "dam"),
                 ascendantSex=c("Male", "Female"), sex="sex"))
  model.matrix(object=x, y=x$pwg, id=x$calf)

Example output

Loading required package: MASS

Attaching package: 'GeneticsPed'

The following object is masked from 'package:stats':

    family

  calf    sex sire  dam pwg
1   S4   Male   S1 <NA> 4.5
2   S5 Female   S3   S2 2.9
3   S6 Female   S1   S2 3.9
4   S7   Male   S4   S5 3.5
5   S8   Male   S3   S6 5.0
  S2 S1 S3 S4 S5 S6 S7 S8
1  0  0  0  1  0  0  0  0
2  0  0  0  0  1  0  0  0
3  0  0  0  0  0  1  0  0
4  0  0  0  0  0  0  1  0
5  0  0  0  0  0  0  0  1

GeneticsPed documentation built on Nov. 8, 2020, 5:54 p.m.