Compute pvalues for the VCC3 method
Description
Compute pvalues for the VCC3 method
Usage
1 2  pvalue.VCC3(P, G, W, Nperm, n, pedigree, haplotypes, generation.id,
Ncores = 1)

Arguments
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). 
Value
the outcomes of the VCC3 association test on the given region, which is a list with the following elements:

score
: The score test 
p.value.VCC2
: The pvalue as output by the VCC2 method (pvalue.VCC2
). 
p.value.VCC3
: This is the exact pvlaue for small level size. The approach to obtain this second pvalue approximates the distribution of the test statistic under the null model by a noncentral chisquare using matching moments of the first, the second and the fourth moments. The estimation of the three moments are approximated empirically using the permutations that were used to calculate the VCC2 pvalue.
Author(s)
Karim Oualkacha
M'Hamed Lajmi LakhalChaieb
See Also
pvalue.VCC1
, pvalue.VCC2
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