RVtests (version 1.0)

RR: Ridge Regression for RV Tests

Description

Use ridge regression for testing rare variants association with disease traits.

Usage

RR(x, y, scale = FALSE, lambda = 1, npermutation = 100, npermutation.max, min.nonsignificant.counts)

Arguments

x

Genotype matrix

y

Phenotype vector

scale

If TRUE, scale x and y.

lambda

Regularization parameter

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
  Correlation between y and y_est
• 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

C. Xu, M. Ladouceur, Z. Dastani, J. B. Richards, A. Ciampi, C. M.T. Greenwood (2012), Multiple regression methods show great potential for rare variant association tests, PLoSONE.

See Also

PCR, PLS