README.md

Build Status Coverage Status CRAN Status

RClone v1.0.2

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


dbailleul/RClone documentation built on May 15, 2019, 1:20 a.m.