GenomicRel: Generate genomic relationship matrix.

In yzhlinscau/AAfun0s: Added Functions for Echidna

Generate genomic relationship matrix.

Description

GenomicRel This function generates 5 genomic relationship matrixs.

option	Description
1	observed allele frequencies (GOF, VanRaden, 2008).
2	weighted markers by recipricals of expected variance (GD, Forni et al., 2011).
3	allele frequencies fixed at 0.5 (G05, Forni et al., 2011).
4	allele frequencies fixed at mean for each locus (GMF, Forni et al., 2011).
5	regression of MM' on A sort (Greg, VanRaden, 2008).

Usage

GenomicRel(marker,option,ped=NULL,
                   Infv=1000,Gm=NULL,G.adj=FALSE,Gres=TRUE)

Arguments

marker	markers data.
option	option (1~5) for different G matrixs.
ped	ped data.
Infv	A value for Inf in G matrix.
Gm	G matrix from marker.
G.adj	Adjust G matrix with A matrix from ped data.
Gres	return G matrix directly(True, default) or in data frame(FALSE).

Author(s)

Isik Fikret

References

Isik Fikret. Genetic data analysis for plant and animal breeding. 2017

Examples

## Not run: 
library(AFEchidna)

read.example(package = "AFEchidna", setpath = TRUE)
Markers<-read.file(file="sim_markers.txt",sep=' ' )
ped<-read.table( "sim_pedigree.txt", sep=' ')


 GOF1=GenomicRel( Markers,1)
 GD1=GenomicRel(  Markers,2)
 G051=GenomicRel( Markers,3)
 GMF1=GenomicRel( Markers,4)
 
 # the same result but adjust G matrix with ped data:
 GOF2=GenomicRel(  Markers,1, ped,G.adj=T)
 GD2=GenomicRel(   Markers,2, ped,G.adj=T)
 G052=GenomicRel(  Markers,3, ped,G.adj=T)
 GMF2=GenomicRel(  Markers,4, ped,G.adj=T)
 Greg=GenomicRel(  Markers,5, ped,G.adj=T)

## End(Not run)

yzhlinscau/AAfun0s documentation built on April 18, 2023, 4:11 p.m.