gprMapping: GPR mapping

In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

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 <[e-mail]>, 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")

BiGGR documentation built on Nov. 8, 2020, 5:38 p.m.