sybilEFBA (version 1.0.2)

gene2Rule: get reaction expression state from gene expression

Description

function to get state of expression of GPR rules from gene expression data

# rules in brief: #1-Complexes: average, 2-isoenzymes: sum #3-multifunctioning: divide by count

N.B.: GPR rules should be in form Sum-of-products (AND to OR)

Usage

gene2Rule(model, geneExpr, selected_rxns = NULL)

Arguments

model

An object of class modelorg.

geneExpr

a data frame: GeneID, expr_val for each gene.

selected_rxns

optional parameter to select only a set of reactions.

Value

return list with main slot:ruleExpr: rxn_id,expr_val

See Also

modelorg, FECorr

Examples

## Not run: 
# ##---- Should be DIRECTLY executable !! ----
# ##-- ==>  Define data, use random,
# ##--	or do  help(data=index)  for the standard data sets.
# 
# ## The function is currently defined as
# function (model, geneExpr, selected_rxns = NULL) 
# {
#     if (length(selected_rxns) == 0) {
#         ugpr = as.vector(unique(gpr(model)))
#     }
#     else {
#         ugpr = as.vector(unique(gpr(model)[selected_rxns]))
#     }
#     ugpr = ugpr[ugpr != ""]
#     gprExpr = NULL
#     for (v_rule in ugpr) {
#         rl = gsub("\)", " ) ", v_rule)
#         rl = gsub("\(", " ( ", rl)
#         pr = lapply(strsplit(unlist(strsplit(rl, " or ")), " and "), 
#             function(x) gsub("[() ]", "", x))
#         expr_val = 0
#         for (p in 1:length(pr)) {
#             gene_ind = match(pr[[p]], geneExpr$geneID)
#             if (length(gene_ind) < length(pr[[p]])) {
#                 warning(sprintf("Rule %s containing gene names not in geneID list, 
# 				term no: %d term: %s ", 
#                   v_rule, p, pr[[p]][1]))
#             }
#             else {
#                 expr_val = expr_val + mean(geneExpr[gene_ind, 
#                   "expr_val"])
#             }
#         }
#         cnt = sum(gpr(model) == v_rule)
#         gprExpr = rbind(gprExpr, cbind(rxn_id = react_id(model)[gpr(model) == 
#             v_rule], expr_val = expr_val/cnt, gpr = v_rule, cnt = rep(cnt, 
#             cnt)))
#     }
#     return(gprExpr)
#   }
# ## End(Not run)