MLL_generator: Clonal Lineage Generation

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

View source: R/RClone.R

Description

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

Usage

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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)

Arguments

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.

Details

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.

Value

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

Author(s)

Creator/Author: Diane Bailleul <[email protected]>
Author: Sophie Arnaud-Haond <[email protected]>
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).

References

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.

See Also

genet_dist

Examples

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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

dbailleul/RClone documentation built on May 12, 2017, 8:56 p.m.