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DRP

R package to calculate deregressed proofs, and its reliabilities and weights.

How to Install

To install this package, use devtools:

devtools::install_github("camult/DRP")

wideDRP: Deregressing estimated breeding values - One wide format file

Description

This package is easy to use and can be helpful to calculate deregressed proofs, and their reliabilities and weights.

Usage

wideDRP(Data, animalId, sireId, damId, c = 0.5, h2, traitName = NULL,
  animalEBV, sireEBV, damEBV, animalr2, sirer2, damr2)

Arguments

Argument Description
Data It is the name of the data file
animalId It is the name of the animal's column
sireId It is the name of the sire's column
damId It is the name of the dam's column
c It is the fraction of genetic variance not explained by markers
h2 It the heritability of the trait
traitName It the name of the trait
animalEBV It is the name of the animal's EBV column
sireEBV It is the name of the sire's EBV column
damEBV It is the name of the dam's EBV column
animalr2 It is the name of the animal's accuracy column
sirer2 It is the name of the sire's accuracy column
damr2 It is the name of the dam's accuracy column

Value

A data frame with deregressed proofs, reliability and weights.

References

Garrick, D. J., J. F. Taylor, and R. L. Fernando. 2009. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet. Sel. Evol. 41:55.

Examples

 ## Not to run ##
 
 ## Example from Garrick et al., (2009)
 
 Dataset=data.frame(animal="A1000", sire="S10", dam="D100", ebv_anim=15, ebv_sire=10, ebv_dam=2,
 r2_anim=0.68, r2_sire=0.97, r2_dam=0.36, trait="Trait", c=0.5, h2=0.25)
 
 wideDRP(Data     =  Dataset,
 animalId  = "animal",
 sireId    = "sire",
 damId     = "dam",
 animalEBV = "ebv_anim",
 sireEBV   = "ebv_sire",
 damEBV    = "ebv_dam",
 animalr2  = "r2_anim",
 sirer2    = "r2_sire",
 damr2     = "r2_dam",
 traitName = "trait",
 c         =  0.5,
 h2        =  0.25)
 
 ## End(Not run)

DRP2files: Deregressing estimated breeding values - Two long format file

Description

This package is easy to use and can be helpful to calculate deregressed proofs, and their reliabilities and weights.

Usage

DRP2files(animalData, parentData, animalCol, sireCol, damCol, parentCol,
  ebvName, r2Name, c = 0.5, h2)

Arguments

Argument Description
animalData It is animal data file
parentData It is parents data file
animalCol It is the name of the animal's column
sireCol It is the name of the animal's dam column
damCol It is the name of the animal's dam column
parentCol It the name of the parents' column in the parents data file
ebvName It is the name of the EBV column
r2Name It is the name of the accuracy column
c It is the fraction of genetic variance not explained by markers
h2 It the heritability of the trait

Value

A data frame with deregressed proofs, reliability and weights.

References

Garrick, D. J., J. F. Taylor, and R. L. Fernando. 2009. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet. Sel. Evol. 41:55.

Examples

 ## Not to run ##
 
 ## Example from Garrick et al., (2009)
 
 animalData=data.frame(ID="Animal", sire="Sire", dam="Dam", EBV=15, r2=0.68)
 parentData=data.frame(ID=c("Sire", "Dam"), EBV=c(10, 2), r2=c(0.97, 0.36))
 
 DRP2files(animalData=animalData,
 parentData=parentData,
 animalCol = "ID",
 sireCol   = "sire",
 damCol    = "dam",
 parentCol = "ID",
 ebvName   = "EBV",
 r2Name   = "r2",
 c         = 0.5,
 h2        = 0.25)
 
 ## End(Not run)