rbt: Replication-Based statistical test

Description Usage Arguments Details Value References Examples

View source: R/rbt.R

Description

Implementation of the replication base test (RBT) proposed by Ionita-Laza et al., 2011. Replication means that it computes evidences to reject each of the two hypothesis: (1) Deleterious rare variants are enriched in cases; (2) Protective rare variants are enriched in controls.

Usage

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rbt(table, perm=150)

Arguments

table

a numeric matrix with first column having disease status '0' or '1' and the rest columns codes the locus genotype as '0', '1', and '2'.

perm

positive integer that defines the number of permutations, 150 by default. In permutation test, the distribution of the test statistic under the null hypothesis is obtained by calculating all possible values of the test statistic under rearrangements of the labels on the observed data points.

Details

....

Value

A list with the following elements:

rbt.stat

RBT statistic

perm.pval

permuted p-value

args

descriptive information with number of controls, cases,variants, and permutations

name

name of the statistic

References

Ionita-Laza I, Buxbaum JD, Laird NM, Lange C (2011) A New Testing Strategy to Identify Rare Variants with Either risk or Protective Effects on Disease. PLoS Genetics, 7(2): e1001289

Examples

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# Load the package

library(vartools)
?rbt

casectrl.dat <- read.table(system.file("extdata","phengen.dat",package="vartools"), skip = 1)
rbt.stat <- rbt(casectrl.dat)
rbt.stat

izhbannikov/vartools documentation built on May 17, 2017, 5:29 a.m.