README.md

In RClone: Partially Clonal Populations Analysis

RClone v1.0.3

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

RClone documentation built on May 15, 2021, 5:07 p.m.