wss: WSS statistical test

Description Usage Arguments Details Value References Examples

View source: R/wss.R

Description

WSS (Madsen and Browning, 2009) is a statistical test, developed for disease traits, in order to test for the hypothesis of rare variants disease association. WSS test introduces the method of assigning "weights" to rare variants found in a genetic region before they are collapsed.

Usage

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wss(table, perm=100)

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. 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:

wss.stat

WSS statistic

asym.pval

asymptotic p-value

perm.pval

permuted p-value; only when permutations is used

args

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

name

name of the statistic

References

Bo Eskerod Madsen and Sharon R. Browning (2009) A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic. PLoS Genetics doi:10.1371/journal.pgen.1000384. http://dx.plos.org/10.1371/journal.pgen.1000384

Examples

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# Load the package

library(vartools)
?wss

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

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