compute.p.snp.obs: Likelihhod ratio test (or Wald test) for an interaction term...

In PIGE: Self Contained Gene Set Analysis for Gene- And Pathway-Environment Interaction Analysis

Description

The compute.p.snp.obs function performs a Likelihood Ratio Test (LRT) for an interaction term SNP*E (where E is an environmental variable) or for the effect of the SNP. The function return the p-value of the Likelihood Ratio Test performed for all the SNPs in the original data set. The SNPs are considered as continuous variable (coded 0,1,2).

Usage

  compute.p.snp.obs(data, Outcome.model = "binary", model,
    indice.snp, var.inter, class.inter = "NULL",
    file.out = "res-obs")

Arguments

data	a data frame containing the variables in the model
model	an object of class "formula": a symbolic description of the model to be fitted without the interaction term
Outcome.model	a character string naming the type of outcome considered. It could be "binary" (by default) or "survival".
indice.snp	vector or character indicating the SNPs to be tested
var.inter	name of the variable which is tested in interaction with the SNPs (SNP:E). By default var.inter=NULL correspond to a test on the SNPs (no interaction)
class.inter	class of the var.inter variable. By default, the variable is considered continuous and a wald test is performed. Use "factor" to indicate a categorical variable.
file.out	name of the output file where the result will be saved.

Value

A data frame with one row containing the pvalue of the likelihood ratio test (or Wald test) for the interaction term (or a SNP effect) for all the SNPs. This data frame is also saved in a txt file (named by the argument file.out) located in the current directory.

Author(s)

Benoit Liquet [e-mail]
Therese Truong [e-mail]

Examples

data(data.pige)
## Case-control study:
data(data.pathway)
data(list.gene.snp)
res <-data.to.PIGE(data=data.pige,data.pathway=data.pathway,
list.gene.snp=list.gene.snp,choice.pathway=c(1,2))
formul <- formula(y~factor(cov1)+factor(cov2)+factor(cov3)+factor(cov4)
+var_int)
p.snp.obs.ex <-  compute.p.snp.obs(data=data.pige,model=formul,
indice.snp=res$snp.selected,var.inter="var_int",class.inter=NULL)

## Survival analysis
data(data.surv)
data(data.pathway.surv)
data(list.gene.snp.surv)
res1 <-data.to.PIGE(data=data.surv,data.pathway=data.pathway.surv,
list.gene.snp=list.gene.snp.surv,choice.pathway=c(1:7))
formul <- formula(Surv(TIME, EVENT) ~ var_int)
p.snp.obs.ex <- compute.p.snp.obs(data=data.surv,Outcome.model="surv"
,model=formul,indice.snp=res1$snp.selected,var.inter="var_int"
,class.inter=NULL,file.out="res-obs-surv")

PIGE documentation built on May 1, 2019, 11:30 p.m.