R package to calculate deregressed proofs, and its reliabilities and weights.
To install this package, use devtools:
devtools::install_github("camult/DRP")
wideDRP
: Deregressing estimated breeding values - One wide format fileThis package is easy to use and can be helpful to calculate deregressed proofs, and their reliabilities and weights.
wideDRP(Data, animalId, sireId, damId, c = 0.5, h2, traitName = NULL,
animalEBV, sireEBV, damEBV, animalr2, sirer2, damr2)
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
A data frame with deregressed proofs, reliability and weights.
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.
## 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
```r
DRP2files(animalData, parentData, animalCol, sireCol, damCol, parentCol,
ebvName, r2Name, c = 0.5, h2)
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
A data frame with deregressed proofs, reliability and weights.
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.
```r ## 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)
```
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