Description Usage Arguments Details Value Author(s) References Examples
View source: R/gen_graph_indep.R
The function allows to create genetic graphs from genetic data by applying the conditional independence principle. Populations whose allelic frequencies covary significantly once the covariance with the other populations has been taken into account are linked on the graphs.
1 2 3 4 5 6 7 8 9 10  gen_graph_indep(
x,
dist = "basic",
cov = "sq",
pcor = "magwene",
alpha = 0.05,
test = "EED",
adj = "none",
output = "igraph"
)

x 
An object of class 
dist 
A character string indicating the method used to compute the multilocus genetic distance between populations

cov 
A character string indicating the formula used to compute the covariance matrix from the distance matrix

pcor 
A character string indicating the way the partial correlation matrix is computed from the covariance matrix.

alpha 
A numeric value corresponding to the statistical tolerance threshold used to test the difference from 0 of the partial correlation coefficients. By default, 'alpha=0.05'. 
test 
A character string indicating the method used to test the significance of the partial correlation coefficients.

adj 
A character string indicating the way of adjusting pvalues to assess the significance of the pvalues

output 
A character string indicating the matrices included in the output list.

The function allows to vary many parameters such as the genetic distance used, the formula used to compute the covariance, the statistical tolerance threshold, the pvalues adjustment, among others.
A list
of objects of class matrix
, an object of
class matrix
or a graph object of class igraph
P. Savary
dyer2004populationgraph4lg \insertRefbenjamini1995controllinggraph4lg \insertRefbowcock1994highgraph4lg \insertRefeveritt2011introductiongraph4lg \insertRefexcoffier1992analysisgraph4lg \insertReffortuna2009networksgraph4lg \insertRefholm1979simplegraph4lg \insertRefmagwene2001newgraph4lg \insertRefwermuth1977algorithmgraph4lg \insertRefwhittaker2009graphicalgraph4lg
1 2 3 4 5  data(data_ex_genind)
dist_graph_test < gen_graph_indep(x = data_ex_genind, dist = "basic",
cov = "sq", pcor = "magwene",
alpha = 0.05, test = "EED",
adj = "none", output = "igraph")

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