RVtests (version 1.0)

VTWOD: VT and WOD for RV Tests

Description

Include methods: T1, T5, WE, VT, and WOD, which were described in the references below.

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, if missing, equal to npermutation.

min.nonsignificant.counts

Minimum nonsignificant counts, if missing, equal to 10.

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

References

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