CNVtest: Testing association between a CNV and phenotype

In CNVassoc: Association Analysis of CNV Data and Imputed SNPs

Description

This function perform a Wald test or a Likelihood Ratio Test (LRT) to determine whether a CNV is associated with the phenotype.

Usage

  CNVtest(x, type = "Wald")
  ## S3 method for class 'CNVtest'
print(x, ...)

Arguments

x	An object of class 'CNVassoc'
type	The statistical test used. Possible values are "Wald" for Wald test or "LRT" for Likelihood Ratio Test
...	Further arguments passed to or from other methods

Value

An object of class 'CNVtest' with methods for the generic function print, returning the Chi-squared value, its degrees of freedom and the corresponding p-value of CNV significance in the associated test fitted by CNVassoc function.

References

Gonzalez JR, Subirana I, Escaramis G, Peraza S, Caceres A, Estivill X and Armengol L. Accounting for uncertainty when assessing association between copy number and disease: a latent class model. BMC Bioinformatics, 2009;10:172.

See Also

CNVassoc,cnv

Examples

data(dataMLPA)
CNV<- cnv(x = dataMLPA$Gene2, threshold.0 = 0.01, mix.method = "mixdist")
mod<-CNVassoc(formula = casco ~ CNV, data = dataMLPA, model = "mul")
CNVtest(mod, type = "LRT")
CNVtest(mod, type = "Wald")

Example output

Loading required package: CNVassocData
Loading required package: mixdist
Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: survival
----CNV Likelihood Ratio Test----
Chi= 18.75453 (df= 2 ) , pvalue= 8.462633e-05 

----CNV Wald test----
Chi= 17.32966 (df= 2 ) , pvalue= 0.0001725492 

CNVassoc documentation built on May 30, 2017, 12:50 a.m.