CNVtest: Testing association between a CNV and phenotype

In isglobal-brge/CNVassoc: Association analysis of CNVs and imputed SNPs incorporating uncertainty

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")

isglobal-brge/CNVassoc documentation built on May 30, 2019, 9:48 p.m.