Defining MLL (MultiLocus Lineage): ascertaining that each distinct MLG (MultiLocus Genotype) belongs to a distinct genet (Halkett et al., 2005a).
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)a Rclone table with one allele per column.
logical, option, haploid indicates the ploidy level of data1.
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.
option, if TRUE, computes genetic distances among MLG in terms of
divergence of microsatellites motifs (Rozenfeld et al., 2007).
option, if TRUE, computes genetic distances among MLG in terms of
weighted divergence of microsatellites motifs (Rozenfeld et al., 2007).
numeric, option, if alpha1 is not NULL, a vertical significativity
line is added on graph at alpha1
numeric, option, if alpha2 is not NULL, a vertical significativity
line is added on graph at alpha2.
table, a result table from genet_dist named potential_clones.
list, a list of MLG, result from MLG_list.
MLL_generator and MLL_generator2 return a list of MLL
(one population) or a list of lists (several populations).
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.
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.
# NOT RUN {
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
# }
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