Annotation gene/SNP

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

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 benoit.liquet@isped.u-bordeaux2.fr
Therese Truong therese.truong@inserm.fr

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(PIGE)
Loading required package: snowfall
Loading required package: snow
Loading required package: ARTP
Loading required package: xtable
Loading required package: survival
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/PIGE/data.to.list.gene.snp.Rd_%03d_medium.png", width=480, height=480)
> ### Name: data.to.list.gene.snp
> ### Title: Annotation gene/SNP
> ### Aliases: data.to.list.gene.snp
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>