gprMappingAvg: GPR mapping ignoring AND & OR operators

In hettling/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. These rules are comprised of AND and OR operators. This function ignores these rules and take average of all genes

Usage

gprMappingAvg(gene_express,react_gene_map)

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

Value

Returns a dataframe with Reaction_id, GPR formulae and average 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.avg<-gprMappingAvg(gene_express,react_gene_map)

hettling/BiGGR documentation built on April 17, 2020, 5:19 a.m.