# PopVar v1.3.0

Monthly downloads

## Genomic Breeding Tools: Genetic Variance Prediction and Cross-Validation

The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations,
from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic
data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all,
or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction
accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015, <doi:10.2135/cropsci2015.01.0030>).
A dataset 'think_barley.rda' is included for reference and examples.

## Readme

# PopVar

## Introduction

To make progress in breeding, populations should have a favorable mean and high genetic variance (Bernardo 2010). These two parameters can be combined into a single measure called the usefulness criterion (Schnell and Utz 1975), visualized in Figure 1.

Ideally, breeders would identify the set of parent combinations that,
when realized in a cross, would give rise to populations meeting these
requirements. `PopVar`

is a package that uses phenotypic and genomewide
marker data on a set of candidate parents to predict the mean, genetic
variance, and superior progeny mean in bi-parental or multi-parental
populations. Thre package also contains functionality for performing
cross-validation to determine the suitability of different statistical
models. More details are available in Mohammadi, Tiede, and Smith
(2015). A dataset `think_barley`

is included for reference and examples.

## Installation

You can install the released version of PopVar from CRAN with:

```
install.packages("PopVar")
```

And the development version from GitHub with:

```
# install.packages("devtools")
devtools::install_github("UMN-BarleyOatSilphium/PopVar")
```

## Functions

Below is a description of the functions provided in `PopVar`

:

Function | Description |
---|---|

`pop.predict` |
Uses simulations to make predictions in recombinant inbred line populations; can internally perform cross-validation for model selections; can be quite slow. |

`pop.predict2` |
Uses deterministic equations to make predictions in populations of complete or partial selfing and with or without the induction of doubled haploids; is much faster than `pop.predict` ; does not perform cross-validation or model selection internally. |

`pop_predict2` |
Has the same functionality as `pop.predict2` , but accepts genomewide marker data in a simpler matrix format. |

`x.val` |
Performs cross-validation to estimate model performance. |

`mppop.predict` |
Uses deterministic equations to make predictions in 2- or 4-way populations of complete or partial selfing and with or without the induction of doubled haploids; does not perform cross-validation or model selection internally. |

`mpop_predict2` |
Has the same functionality as `mppop.predict` , but accepts genomewide marker data in a simpler matrix format. |

## Examples

Examples are outlined in the package vignette.

## References

*Breeding for Quantitative Traits in Plants*. 2nd ed. Woodbury, Minnesota: Stemma Press.

*Crop Science*55 (5): 2068–77. https://doi.org/10.2135/cropsci2015.01.0030.

*Bericht über Die Arbeitstagung Der Vereinigung Österreichischer Pflanzenzüchter*, 243–48. Gumpenstein, Austria: BAL Gumpenstein.

## Functions in PopVar

Name | Description | |

mppop.predict | Predict genetic variance and genetic correlations in multi-parent populations using a deterministic equation. | |

pop.predict2 | Predict genetic variance and genetic correlations in bi-parental populations using a deterministic model | |

PopVar-package | Genomic breeding tools to 1) predict standard statistics and correlated response in plant populations, and 2) performs cross-validation to estimate genome-wide prediction accuracy | |

x.val | Estimate genome-wide prediction accuracy using cross-validation | |

internal | Internal functions | |

think_barley.rda | An example barley dataset | |

pop.predict | A genome-wide procedure for predicting genetic variance and correlated response in bi-parental breeding populations | |

No Results! |

## Vignettes of PopVar

Name | ||

figures/figure1.png | ||

popvar_walkthrough.Rmd | ||

No Results! |

## Last month downloads

## Details

License | GPL-3 |

Encoding | UTF-8 |

LazyData | true |

RoxygenNote | 7.1.1 |

VignetteBuilder | knitr |

NeedsCompilation | no |

Packaged | 2021-01-13 19:20:51 UTC; jln54 |

Repository | CRAN |

Date/Publication | 2021-02-07 20:10:17 UTC |

imports | BGLR , methods , parallel , qtl , rrBLUP , stats , utils |

suggests | knitr , rmarkdown |

depends | R (>= 3.5.0) |

Contributors | Tyler Tiede, Mohsen Mohammadi, Kevin Smith |

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