duydn / drp

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

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)