VTWOD: VT and WOD for RV Tests

In RVtests: Rare Variant Tests

Description

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

Usage

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

RVtests documentation built on May 1, 2019, 9:51 p.m.