gprMapping {BiGGR} | R Documentation

## GPR mapping

### Description

Continuous gene expression levels are mapped from genes to reactions using the gene-protein-reaction (GPR) association rules as found in ReconX databases. The expression level of reactions catalyzed by enzyme complexes (`and` operator) can be set to the minimum,maximum,mean and median functions. Similarly expression level of the associated genes, and the expression level of reactions catalyzed by isoenzymes (`or` operator) can also be set to either minimum,maximum,mean and median functions for the associated genes. Operator Precedence: "AND" followed by "OR"

### Usage

    gprMapping(gene_express,react_gene_map,OR=c("mean","median","min","max"),AND=c("min","max","mean","median"))

### Arguments

`gene_express` | The path to a gene expression file with three columns gene_symbol,entrez_id and foldchanges
`react_gene_map` | Database file created from ReconX database using functions such as `rmvSpliceVariant`
`OR` | Takes values from statistical functions such as `mean`,`median`,`min`,`max`
`AND` | Takes values from statistical functions such as `mean`,`median`,`min`,`max`

### Value

Returns a dataframe with Reaction_id, GPR formulae and Calculated values

### Author(s)

Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling

### Examples

    # Read gene expression data
    file <- system.file("extdata", "Gene_Symbol_Entrez_Foldchanges.csv", package="BiGGR")
    gene_express<-read.csv(file,header=TRUE)
    data(Recon2)
    gene.info <- extractGeneAssociations(Recon2)

    gene.info<-do.call(rbind.data.frame,gene.info)
    colnames(gene.info)<-c("GPR")
    gene.info$react_id<-row.names(gene.info)
    gene.info<-gene.info[,c(2,1)]
    rownames(gene.info)<-NULL
    react_gene_map<-rmvSpliceVariant(gene.info)

    gpr.map<-gprMapping(gene_express,react_gene_map,OR="mean",AND="min")

[Package BiGGR version 1.20.0 Index]