bootstrap.snp: Parallel computing of the Likelihhod ratio test (or Wald...

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

Description

The bootstrap.snp function performs on bootstrap sample a Likelihood Ratio Test (or a Wald test) for an interaction term SNP*E (where E is an Environment variable) or for the effect of the SNP. This function uses the parallel computing on different CPU of the computer. This function returns a matrix containing for each bootstrap and SNP the p-value of the interaction term tested (SNP*E) or the p-value of the SNP effect tested. Note that this parametric bootsrap approach has been only currently implemented in this package for Logistic model.

Usage

  bootstrap.snp(model, Outcome.model = "binary", data,
    var.inter = NULL, indice.snp, class.inter = NULL,
    nbcpu = NULL, Nboot = 1000,file.out = "res-boot")

Arguments

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. The current version allows only "binary" (by default).
data	a data frame containing the variables in the model.
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)
indice.snp	vector or character indicating the SNPs to be tested.
class.inter	class of the var.inter variable. By default, the variable is considered as continuous and a Wald test is performed. Use ("factor") to indicate categorical variable.
nbcpu	integer indicating the number of CPU of your computer (-1). By default, the function use only one cpu.
Nboot	number of bootstrap (1000 by default).
file.out	name of the output file where the result will be saved.

Value

A matrix containing the p-value, for each bootstrap (row) and for each SNP (column), of the likelihood ratio test (or the Wald test) for the interaction term or the SNP effect. This matrix 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)
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)
debut <- Sys.time()
p.snp.boot.ex <-  bootstrap.snp(model=formul,data=data.pige,
indice.snp=res$snp.selected,var.inter="var_int",class.inter=NULL,
nbcpu=2,Nboot=2,file.out="res-boot")
print(Sys.time()-debut)

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