gprMappingAvg: GPR mapping ignoring AND & OR operators

Description Usage Arguments Value Author(s) Examples

View source: R/gprMappingAvg.R

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

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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 <anand.gavai@bioinformatics.nl>, Hannes Hettling

Examples

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# 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)

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