PIGE (version 1.1)

data.to.PIGE: Generate data for Gene- and Pathway-environment interaction

Description

The data.to.PIGE function prepare your data to be analysed by the functions permutation.snp and compute.p.snp.obs.

Usage

data.to.PIGE(data, data.pathway, list.gene.snp,
    choice.pathway = NULL)

Arguments

data

a data frame containing the variables in the model and the SNP.

data.pathway

A data frame (Gene X Pathway) of 0 and 1 values. The rownames (gene name considered) and the colnames (names of the studied pathways). have to be specified. The value 1 indicates that a gene is included in the corresponding pathway.

list.gene.snp

List containing for each gene the names of the SNPs belonging to it. This list could be generated by data.to.list.gene.snp function.

choice.pathway

names or indice of the pathway to be analysed.

Value

The returned value is a list containing:

data.pathway

A data frame (Gene X Pathway) of 0 and 1 values similar as data.pathway but only for the selected pathways.

tab.snp.gene

A matrix with in the first column the names of the SNPs and the corresponding gene on the second column. Note that a SNPs could belong to several gene.

snp.selected

A vector of names corresponding to the SNPs analalysed.

Examples

# NOT RUN {
data(data.pathway)
data(data.pige)
data(list.gene.snp)
#Example: one pathway
res1 <-data.to.PIGE(data=data.pige,data.pathway=data.pathway,
list.gene.snp=list.gene.snp,choice.pathway=c(2))
#Example: two pathways
res <-data.to.PIGE(data=data.pige,data.pathway=data.pathway
,list.gene.snp=list.gene.snp,choice.pathway=c(1,2))
# }