RVtests (version 1.2)

RR: Ridge Regression for RV Tests

Description

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

Usage

RR(x, y, z = NULL, scale = FALSE, weights = 1, lambda = 1, 
	npermutation = 1000, npermutation.max, min.nonsignificant.counts = 100)

Arguments

x

Genotype matrix

y

Phenotype vector

z

Covariate matrix

scale

If TRUE, scale x and y.

weights

Genotype weights

lambda

Regularization parameter

npermutation

Number of permutation

npermutation.max

Maximum permutation

min.nonsignificant.counts

Minimum nonsignificant counts

Value

nonsignificant.counts

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

total.permutation

Total permutation

score

Correlation between y and y_est if z=NULL.

pvalue.empirical

Empirical pvalue via permutation

pvalue.nominal

Theoretical pvalue, not available.

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

See Also

PCR, PLS