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

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

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.

Author(s)

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

Examples

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))

Example output

Loading required package: snowfall
Loading required package: snow
Loading required package: ARTP
Loading required package: xtable
Loading required package: survival
Perfect all the snp considered belong to the data framePerfect all the snp considered belong to the data frame

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