PIGE (version 1.1)

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

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.

Examples

# NOT RUN {
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")
# }