pvalue.VCC2: Compute the p-value for the VC-C2 method
In RVPedigree: Methods for Family-Based Rare-Variant Genetic Association Tests

Description Usage Arguments Value Author(s) See Also

Compute the p-value for the VC-C2 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 `Preparation.VCC`.
`G`	the genotype matrix
`Nperm`	(integer) The number of permutations to be done to calculate the empirical p-value 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 `read.pedigree`. This is a data frame consisting of four columns (family ID, individual ID, father ID and mother ID) as use in the traditional linkage format and e.g. Plink files.
`haplotypes`	a matrix of the haplotypes of the individuals
`generation.id`	a vector of length(sample size) which indicates if the subject is founder (`generation.id=0`), a child from first generation (`generation.id=1`), a child from second generation (`generation.id=2`), etc. This vector can be calculated by the `kinship2::kindepth()` function.
`Ncores`	(integer) Number of processor (CPU) cores to be used in parallel when doing the permutations to determine the p-value (default: 1).

a list with the score and p-value for the VC-C2 association test on the given region. The list contains the elements score and p.value. This is a permutation-based p-value.

Karim Oualkacha

M'Hamed Lajmi Lakhal-Chaieb

pvalue.VCC1, pvalue.VCC3

RVPedigree documentation built on May 29, 2017, 10:19 p.m.