Description Usage Arguments Value Author(s) See Also
Compute the pvalue for the VCC2 method
1 2  pvalue.VCC2(P, G, W, Nperm, n, pedigree, haplotypes, generation.id,
Ncores = 1)

P 
a matrix which can be obtained as output of the function

G 
the genotype matrix 
Nperm 
(integer) The number of permutations to be done to calculate the empirical pvalue if the VCC2 or VCC3 method is used. For other methods this parameter is ignored (default: 100). 
n 
Integer, the number of samples 
pedigree 
a pedigree as output by

haplotypes 
a matrix of the haplotypes of the individuals 
generation.id 
a vector of length(sample size) which
indicates if the subject is founder ( 
Ncores 
(integer) Number of processor (CPU) cores to be used in parallel when doing the permutations to determine the pvalue (default: 1). 
a list with the score and pvalue for the VCC2
association test on the given region. The list contains the
elements score
and p.value
. This is a
permutationbased pvalue.
Karim Oualkacha
M'Hamed Lajmi LakhalChaieb
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