RVtests (version 1.2)

RVtests-package: Rare Variants Tests

Description

Use multiple regression methods to test rare variants association with disease traits.

Details

Package:

RVtests

Type:

Package

Version:

1.2

Date:

2013-05-27

License:

GLP 2.0 or greater

LazyLoad:

yes

An overview of how to use the package, including the most important functions

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

Examples

data(sample.cgeno)
str(sample.cgeno) 
x=count2geno(sample.cgeno$cgeno)
dim(x)

set.seed(31018)
y<- rowSums(x[,2:4]*rep(rnorm(3,1,0.1), each=nrow(x))) + 0.4*rnorm(nrow(x))

tmp<- proc.time();RR(x,y,lambda=0:5); proc.time()-tmp
tmp<- proc.time();RR(x,y,weights=c(rep(2,10), rep(1, ncol(x)-10)), lambda=0:5); proc.time()-tmp
tmp<- proc.time();RR(x,y,weights=c(rep(1,10), rep(0, ncol(x)-10)), lambda=0:5); proc.time()-tmp