Ginv: G inverse matrices output

In yzhlinscau/AAfun: ASReml-R Added functions

Description

This function generates G matrices using different methods

Usage

Ginv(marker.file, ped.file, aped.rowNames, path = NULL, Goptions = 1)

Arguments

marker.file	The marker file, first column is id then SNPs, SNPs must be 0,1,2.
ped.file	The pedigree file, contains id, sire(or female) and dam (or male).
aped.rowNames	The rowNames of pedigree inverse matrix.
path	The path of all datasets for GBLUP.
Goptions	G matrices for different methods,1(default) using frequencies,2 using regression.

Value

marker.file	marker.file="Genotype.csv"
ped.file	ped.file="pedigree.csv"
path	path="G:\Users\yzhlin\GBLUP"
Goptions	Goptions=1, or 2

Author(s)

Yuanzhen Lin <[e-mail]>

References

1. VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci,2008, 91: 4414-4423. 2. Yuanzhen Lin. R & ASReml-R Statistics. China Forestry Publishing House. 2016

See Also

Website for instant update: yzhlin-asreml.ys168.com

Examples

library(asreml)
library(AAfun)

#### for demo examples
data(G.data)
data(G.pedigree)
data(G.marker)

gpedinv=asreml.Ainverse(G.pedigree)$ginv
gpnames=attributes(gpedinv)$rowNames

Ginv1=Ginv(marker.file=G.marker,ped.file=G.pedigree,aped.rowNames=gpnames,Goptions=1)

gblup<-asreml(t1~1+Site,random=~ giv(ID), ## ped(ID)
               ginverse=list(ID=Ginv1),data=G.data)

summary(gblup)$varcomp
c<-coef(gblup)$random

#### for user

df<-asreml.read.table("data.csv",T,",")
aped<-asreml.read.table("pedigree.csv",T,",")
apedinv=asreml.Ainverse(aped)$ginv
apnames=attributes(apedinv)$rowNames 

path="G:/Users/yzhlin/Desktop/GBLUP"
Ginv1=Ginv(marker.file="Genotype.csv",ped.file="pedigree.csv",
                       aped.rowNames=apnames,path=path,Goptions=1)

## GBLUP
df.asr<-asreml(t1~1+Site,random=~ giv(ID),
               ginverse=list(ID=Ginv1),data=df)

## ABLUP
df2.asr<-asreml(t1~1+Site,random=~ ped(ID),
               ginverse=list(ID=apedinv),data=df)               

summary(df.asr)$varcomp
summary(df2.asr)$varcomp

yzhlinscau/AAfun documentation built on May 21, 2020, 2:19 p.m.