Partially Clonal Populations Analysis

R version of 'GenClone' (a computer program to analyse genotypic data, test for clonality and describe spatial clonal organization, Arnaud-Haond & Belkhir 2007, < http://wwz.ifremer.fr/clonix/content/download/68205/903914/file/GenClone2.0.setup.zip>), this package allows clone handling as 'GenClone' does, plus the possibility to work with several populations, MultiLocus Lineages (MLL) custom definition and use, and p-value calculation for psex statistic (probability of originating from distinct sexual events) and psex_Fis statistic (taking account of Hardy-Weinberg equilibrium departure) as 'MLGsim'/'MLGsim2' (a program for detecting clones using a simulation approach, Stenberg et al. 2003).


Build Status Coverage Status CRAN Status

RClone is a R package version of GenClone program: to analyse data (SSR, SNP, ...), test for clonality and describe spatial clonal organisation.

RClone allows:

  1. Description of data set
    • discrimination of MLG (MultiLocus Genotypes);
    • test for reliability of data (in terms of loci and sampling).
  2. Determination of MLL (MultiLocus Lineages)
    • psex/psex Fis with pvalue computation;
    • genetic distance matrix computation and threshold definition.
  3. Genotypic diversity and evenness indices calculation
    • Simpson complement;
    • Shannon-Wiener diversity and evenness indices;
    • Hill's Simpson reciprocal;
    • Pareto index.
  4. Spatial organisation of MLG/MLL
    • spatial autocorrelation methods;
    • clonal subrange estimation;
    • Aggregation index and Edge Effect estimation.

Some of these analysis can be applied to dataset without clones.

Installation

Get the lastest development version from github:

#install.packages("devtools")
devtools::install_github("dbailleul/RClone")
library(RClone)

or the released version from CRAN:

install.packages("RClone")

And then, generate manuals:

vignette("RClone_quickmanual") #analysing one population
vignette("RClone_qmsevpops") #analysing several populations

News

Reference manual

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install.packages("RClone")

1.0.2 by Diane Bailleul, 3 years ago


https://github.com/dbailleul/RClone


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


Authors: Sophie Arnaud-Haond [aut] , Diane Bailleul [aut, cre] , Solenn Stoeckel [ctb]


Documentation:   PDF Manual  


GPL (>= 2.0) license


Depends on graphics, stats, grDevices, utils, datasets, methods

Suggests knitr, pander, testthat


Suggested by poppr.


See at CRAN