RR: Ridge Regression for RV Tests

In RVtests: Rare Variant 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.

Author(s)

C. Xu

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

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