SNP Genotype Marker Design and Analysis

We implement a common genotyping workflow with a standardized software interface. 'genotypeR' designs genotyping markers from vcf files, outputs markers for multiplexing suitability on various platforms (Sequenom and Illumina GoldenGate), and provides various QA/QC and analysis functions. We developed this package to analyze data in Stevison LS, SA Sefick, CA Rushton, and RM Graze. 2017. Invited Review: Recombination rate plasticity: revealing mechanisms by design. Philosophical Transactions Royal Society London B Biol Sci 372:1-14. , and have published it here Sefick, S.A., M.A. Castronova, and L.S. Stevison. 2017. GENOTYPER: An integrated R packages for single nuleotide polymorphism genotype marker design and data analysis. Methods in Ecology and Evolution 9: 1318-1323. .


DOI

This contains the development of the genotypeR R package. genotypeR implements a common genotyping workflow with a standardized software interface. genotypeR designs genotyping markers from vcf files, outputs markers for multiplexing suitability on various platforms (Sequenom and Illumina GoldenGate), and provides various QA/QC and analysis functions. This package can be installed from the github repository using devtools. This package will also be avaliable on CRAN, and can be installed in the usual way.

devtools::install_git("https://github.com/StevisonLab/genotypeR", build_vignette=TRUE)
 

If it is desirable to only use the PERL pipeline without the rest of the R package that is possible as well.

Citations

Sefick, S.A., M.A. Castronova, and L.S. Stevison. 2017. GENOTYPER: An integrated R packages for single nuleotide polymorphism genotype marker design and data analysis. Methods in Ecology and Evolution 9: 1318-1323. <DOI: 10.1111/2041-210X.12965>

Package developed to analyze: Stevison LS, SA Sefick, CA Rushton, and RM Graze. 2017. Invited Review: Recombination rate plasticity: revealing mechanisms by design. Philosophical Transactions Royal Society London B Biol Sci 372:1-14. <DOI: 10.1098/rstb.2016.0459>

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Reference manual

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install.packages("genotypeR")

0.0.1.8 by Stephen Alfred Sefick, 9 months ago


https://github.com/StevisonLab/genotypeR


Browse source code at https://github.com/cran/genotypeR


Authors: Stephen Alfred Sefick [aut, cre] , Magdelena A Castronova [aut] , Laurie S Stevison [aut]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports methods, reshape2, plyr, doBy, zoo, colorspace

Suggests testthat, knitr, rmarkdown, qtl

System requirements: The SequenomMarkers() marker design function requires 'vcftools' and 'Perl' on 'windows', and, in addition, 'awk' and 'bash' on '*nix'.


See at CRAN