MLL_generator: Clonal Lineage Generation
In RClone: Partially Clonal Populations Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

Defining MLL (MultiLocus Lineage): ascertaining that each distinct MLG (MultiLocus Genotype) belongs to a distinct genet (Halkett et al., 2005a).

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MLL_generator(data1, haploid = FALSE, vecpop = NULL, manh = FALSE, manh_w = FALSE, 
		alpha1 = NULL, alpha2 = NULL)
MLL_generator2(potential_clones = NULL, res_mlg = NULL, vecpop = NULL)

`data1`	a `Rclone` table with one allele per column.
`haploid`	logical, option, `haploid` indicates the ploidy level of `data1`.
`vecpop`	vector, option, `vecpop` indicates the population name of each unit of `data1`, if `data1` contains several populations. If `data1` contains only one population, leave `vecpop = NULL`.
`manh`	option, if `TRUE`, computes genetic distances among MLG in terms of divergence of microsatellites motifs (Rozenfeld et al., 2007).
`manh_w`	option, if `TRUE`, computes genetic distances among MLG in terms of weighted divergence of microsatellites motifs (Rozenfeld et al., 2007).
`alpha1`	numeric, option, if `alpha1` is not NULL, a vertical significativity line is added on graph at `alpha1`
`alpha2`	numeric, option, if `alpha2` is not NULL, a vertical significativity line is added on graph at `alpha2`.
`potential_clones`	table, a result table from `genet_dist` named `potential_clones`.
`res_mlg`	list, a list of MLG, result from `MLG_list`.

MLL_generator creates automatically MLL from a given genetic distance (alpha2) or a percentage of the distribution of genetic distance (alpha1).

If several populations (vecpop != NULL), MLL_generator is the only function in the package RClone to accept different arguments for an option. alpha1 and alpha2 thus are vectors of several numeric values, one per populations.

If manh = TRUE or manh_w = TRUE, divergence of SSR motifs (Rozenfeld et al., 2007) is used as genetic distance.

MLL_generator2 computes a list of MLL from previous results of genet_dist and MLG_list.

MLL_generator and MLL_generator2 compute a list of MLL to use with others RClone functions.

MLL_generator and MLL_generator2 return a list of MLL (one population) or a list of lists (several populations).

Creator/Author: Diane Bailleul <diane.bailleul.pro@gmail.com>
Author: Sophie Arnaud-Haond <sophie.arnaud@ifremer.fr>
Contributor: Solenn Stoeckel

The R implementation of RClone was written by Diane Bailleul.

The design was inspired by GenClone program described in Arnaud-Haond & Belkhir (2007).

Chakraborty & Jin, 1993, Determination of relatedness between individuals using DNA-fingerprinting.

Arnaud-Haond et al., 2007, Standardizing methods to address clonality in population studies.

Rozenfeld et al., 2007, Spectrum of genetic diversity and networks of clonal populations.

genet_dist

data(popsim)

#MLLlist <- MLL_generator(popsim, alpha2 = 4)
#or
#res <- genet_dist(popsim, alpha2 = 4)
#MLLlist <- MLL_generator2(res$potential_clones, MLG_list(popsim))
#take few seconds