Skip to main content
Log in

snpReady: a tool to assist breeders in genomic analysis

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

The snpReady R package is a new instrument developed to help breeders in genomic projects such as genomic prediction and association studies. This package offers three different methods to build the genomic relationship matrix, a new imputation method for missing markers based on Wright’s theory, and a population genetic overview. Therefore, we implemented three functions (raw.data, G.matrix, and popgen). Hence, this tool allows the raw data to be transformed from different genotyping platforms to numeric matrices and performs quality control (missing data and allele frequency). Moreover, the package generates and exports four different relationship matrices (proposed by Yang et al. (N 569:565–569, 2010), VanRaden (JDS 91:4414–23, 2008), and the Gaussian kernel) depending on the purpose and software to be used in further analysis. Finally, based on the genotypic matrix, the package estimates the genetic variability, effective population size, and endogamy, among other population genetic parameters. Empirical comparisons between the method of imputation proposed and other well-known approaches have shown a lower accuracy of imputation, however, with no significant impact on the genome prediction accuracies when a lower amount of missing data is allowed. The functions and arguments were designed to carry out the preparation of genomic datasets in a straightforward, fast, and more computationally efficient way.

The package and its details are available at CRAN or http://www.github.com/italo-granato/snpReady.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

Download references

Funding

The authors thank the National Council for Scientific and Technological Development (CNPq) and Coordination for the Improvement of Higher Level Personnel (CAPES) for granting scholarships that allowed the creation of this tool.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Italo S. C. Granato.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Granato, I.S.C., Galli, G., de Oliveira Couto, E.G. et al. snpReady: a tool to assist breeders in genomic analysis. Mol Breeding 38, 102 (2018). https://doi.org/10.1007/s11032-018-0844-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-018-0844-8

Keywords

Navigation