proxecat_over: Overdispersed ProxECAT

Description Usage Arguments Value Examples

Description

Runs the overdispersed Proxy External Controls Association Test (ProxECAT) method given the number of rare alleles in each gene region and an overdispersion parameter

Usage

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proxecat_over(x1, x2, x3, x4, size = 1000)

Arguments

x1

vector of the number of functional rare alleles in cases for each gene region

x2

vector of the number of synonymous rare alleles (or other proxy) in cases for each gene region

x3

vector of the number of functional rare alleles in controls for each gene region

x4

vector of the number of synonymous rare alleles (or other proxy) in controls for each gene region

size

overdispersion parameter. The smaller size, the more over dispersed. The larger size the less overdispersed. Size of >1000 is approximately Poisson.

Value

input data, likelihood ratio test statistic and p-value for overdispersed ProxECAT. LRT is asymptotically chi-squared with 1 df.

Examples

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##runs overdispersed proxy-ECAT for 5 gene regions
x1<-c(12,10,5,103,89)
x2<-c(6,5,3,10,3)
x3<-c(20,20,8,5,8)
x4<-c(9,11,8,7,3)
temp<-proxecat_over(x1=x1, x2=x2, x3=x3, x4=x4, size=100)
temp

hendriau/ProxECAT documentation built on May 31, 2019, 8:41 a.m.