gprMappingAvg {BiGGR} | R Documentation |
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
gprMappingAvg(gene_express,react_gene_map)
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 |
Returns a dataframe with Reaction_id, GPR formulae and average values
Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling
# 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)