vt: Variable Threshold statistical test

Description Usage Arguments Details Value References Examples

View source: R/vt.R

Description

This is implementation for the Variable Threshold statistical test. It assigns different weights to rare variants base on their frequencies.

Usage

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vt(table, maf=0.05, perm=50)

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'.

maf

numeric value indicating the minor allele frequency threshold for rare variants (must be a positive number between 0 and 1, maf=0.05 by default).

perm

positive integer that defines the number of permutations, perm=50 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:

vt.stat

VT statistic

perm.pval

permuted p-value

args

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

name

name of the statistic

References

Price AL, Kryukov GV, de Bakker PIW, Purcell SM, Staples J, Wei LJ, Sunyaev SR (2010) Pooled Association Tests for Rare Variants in Exon-Sequencing Studies. The American Journal of Human Genetics, 86: 832-838

Examples

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# Load the package
library(vartools)
?vt

casectrl.dat <- read.table(system.file("extdata","phengen2.dat",package="vartools"), skip = 1)
vt.stat <- vt(casectrl.dat)
vt.stat

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