PopGenReport: simplifying basic population genetic analyses in R

Aaron ADAMACK, Bernd GRUBER

    Research output: Contribution to journalArticle

    109 Citations (Scopus)

    Abstract

    1. Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but usingRcan be challenging for many researchers due to its steep learning curve. 2. POPGENREPORT 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 inmultiple formats, table contents are provided as CSV files). 3. 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 (1999) andKosman and Leonard (2005), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall (1999). 4. 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. 5. 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.
    Original languageEnglish
    Pages (from-to)384-387
    Number of pages4
    JournalMethods in Ecology and Evolution
    Volume5
    Issue number4
    DOIs
    Publication statusPublished - 2014

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    population genetics
    allele
    alleles
    null alleles
    population distribution
    autocorrelation
    reproducibility
    genetic distance
    learning
    researchers
    spreadsheet
    loci
    genotype
    methodology
    testing
    method
    test
    analysis

    Cite this

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    title = "PopGenReport: simplifying basic population genetic analyses in R",
    abstract = "1. Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but usingRcan be challenging for many researchers due to its steep learning curve. 2. POPGENREPORT 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 inmultiple formats, table contents are provided as CSV files). 3. 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 (1999) andKosman and Leonard (2005), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall (1999). 4. 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. 5. 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.",
    keywords = "ecological genetics, population genetics, software, bioinformatics, quantitative genetics, individual pairwise genetic distances.",
    author = "Aaron ADAMACK and Bernd GRUBER",
    year = "2014",
    doi = "10.1111/2041-210X.12158",
    language = "English",
    volume = "5",
    pages = "384--387",
    journal = "Methods in Ecology and Evolution",
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    }

    PopGenReport: simplifying basic population genetic analyses in R. / ADAMACK, Aaron; GRUBER, Bernd.

    In: Methods in Ecology and Evolution, Vol. 5, No. 4, 2014, p. 384-387.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - PopGenReport: simplifying basic population genetic analyses in R

    AU - ADAMACK, Aaron

    AU - GRUBER, Bernd

    PY - 2014

    Y1 - 2014

    N2 - 1. Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but usingRcan be challenging for many researchers due to its steep learning curve. 2. POPGENREPORT 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 inmultiple formats, table contents are provided as CSV files). 3. 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 (1999) andKosman and Leonard (2005), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall (1999). 4. 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. 5. 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.

    AB - 1. Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but usingRcan be challenging for many researchers due to its steep learning curve. 2. POPGENREPORT 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 inmultiple formats, table contents are provided as CSV files). 3. 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 (1999) andKosman and Leonard (2005), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall (1999). 4. 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. 5. 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.

    KW - ecological genetics

    KW - population genetics

    KW - software

    KW - bioinformatics

    KW - quantitative genetics

    KW - individual pairwise genetic distances.

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    DO - 10.1111/2041-210X.12158

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    JO - Methods in Ecology and Evolution

    JF - Methods in Ecology and Evolution

    SN - 2041-210X

    IS - 4

    ER -