VT and WOD for RV Tests

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Description

Include methods: T1, T5, WE, VT, and WOD.

Usage

1
2
VTWOD(x, y, polyphen.weight, flipPhenotype = 0, 
	npermutation = 1000, npermutation.max, min.nonsignificant.counts)

Arguments

x

Genotype matrix

y

Phenotype vector

polyphen.weight

Polyphen weight

flipPhenotype

Logical, if TRUE, flip phenotype to opposite by multipling -1

npermutation

Number of permutation, if less than 1, the permutation will not be run.

npermutation.max

Maximum permutation

min.nonsignificant.counts

Minimum nonsignificant counts

Value

score

Scores of T1, T5, WE, VT, and WOD

nonsignificant.counts

Counts of permuted data that have a higher score than unpermuted data.

pvalue.empirical

Empirical pvalue via permutation

pvalue.nominal

Theoretical pvalue, not available now.

total.permutation

Total permutation

Note

This R implementation by Adam Kiezun, based on reference implementation in C by Alkes Price. Added WOD tests to the program in 2011 by Celia Greenwood

Author(s)

C. Xu, Celia Greenwood

References

Xu C, Ladouceur M, Dastani Z, Richards JB, Ciampi A, Greenwood CMT. (2012) Multiple Regression Methods Show Great Potential for Rare Variant Association Tests. PLoS ONE 7(8): e41694. doi:10.1371/journal.pone.0041694

Ladouceur M, Dastani Z, Aulchenko YS, Greenwood CM, Richards JB (2012) The empirical power of rare variant association methods: Results from sanger sequencing in 1,998 individuals. PloS Genetics 8: e1002496.

Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, et al. (2010) Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86: 832 - 838.

See Also

RR, PCR, PLS