data.to.list.gene.snp: Annotation gene/SNP

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

Description

The data.to.list.gene.snp function generates the list containing for each gene the corresponding SNP ids from a txt file containing the SNP/gene annotation data. This list is required for the functions data.to.PIGE and ARTP.GE.

Usage

  data.to.list.gene.snp(file, header = TRUE, path = NULL)

Arguments

file	txt file containing the SNP/gene annotation (see Details for the format of the txt file).
header	a logical value indicating whether the file contains the names of the variables as its first line. By default header is set to TRUE.
path	linking to the directory containing the data (SNP/gene)

Details

The txt file containing the annotation data for the SNP/gene is a two columns matrix. The first colums is the name of each SNP. The second columns indicates the genes which the corresponding SNP (same row) belongs. It will be noted "Gene1/Gene4/Gene5", if for example a SNP belongs to the genes: Gene1, Gene4, Gene5.

Value

A list containing for each gene the names of the SNPs belonging to it. This list is required for using the function data.to.PIGE and the function ARTP.GE.

Author(s)

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

Examples

##Example : case-control study data
data(data.pige)
data(data.pathway)
path.in <- paste(system.file("sampleData", package="PIGE"),"/",sep="")
file <- "SNP-GENE-annotation.txt"
list.gene.snp <- data.to.list.gene.snp(file,path=path.in)
##Example Survival data
data("data.surv")
data("data.pathway.surv")
path.in <- paste(system.file("sampleData", package="PIGE"),"/",sep="")
file="snp.gene.surv.txt"
list.gene.snp.surv <- data.to.list.gene.snp(file,path=path.in)

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