P<scp>op</scp>G<scp>en</scp>R<scp>eport</scp>: simplifying basic population genetic analyses in R 论文

详细信息

发表期刊/会议

Methods in Ecology and Evolution

发表日期

2014-01-15

发表年份

2014

摘要

Summary Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but using R can be challenging for many researchers due to its steep learning curve. P op G en R eport is a new R package that simplifies performing population genetics analyses in R, through the use of a new report‐generating function. The function popgenreport allows users to perform up to 13 pre‐defined and 1 user‐defined analyses through the use of a single command line. Each analysis generates figures and tables that are incorporated into a pdf report and are also made available as individual files (figures are provided in multiple formats, table contents are provided as csv files). The package includes new R functions that simplify the importation of data from a spreadsheet file, examine allele distributions across populations and loci and identify private alleles, determine pairwise individual genetic distances using the methods of Smouse and Peakall ( ) and Kosman and Leonard ( ), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall ( ). The package has a modular structure that makes the process of adding new functionality straightforward. To facilitate the addition of user‐designed functions, the package includes a fully customizable module that can be automatically included in the pdf report. To support users not experienced in R, the website ( www.popgenreport.org ) has a tutorial for the package and a downloadable, portable version of the package with LaTeX pre‐configured for the Windows operating system.