asum: aSum statistical test

Description Usage Arguments Details Value References Examples

View source: R/asum.R

Description

aSum, Adaptive Sum Test (Han and Pan, 2010) is a statistical test which utilizes the difference in direction of effects (protective or deleterious) of rare variants within the same genetic region analyzed by a rare variant association test.

Usage

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asum(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:

asum.stat

aSum statistic

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

Fang Han and Wei Pan (2010) A Data-Adaptive Sum Test for Disease Association with Multiple Common or Rare Variants. Human Heredity doi:10.1159/000288704. http://www.karger.com/doi/10.1159/000288704

Examples

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# Load the package

library(vartools)
?asum

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

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