build_sif_table_from_rule: Build a SIF table from a logic rule written in a string

In saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Build a SIF table from a logic rule written in a string

Description

Build a SIF table from a logic rule written in a string

Usage

build_sif_table_from_rule(rule_str, target, last_and_num = 0)

Arguments

rule_str	String containing the rule to be parsed
target	Name of the node affected by the rule
last_and_num	If the rule contains 'and' gates, their numeration will start after the number provided here (default is 0)

Value

data.frame with the network structure derived from the rule. The column 'sif_str' contains the string that can be written to a file and then read with 'readSIF()' in order to load a CellNOpt compatible network.

Examples

CellNOptR:::build_sif_table_from_rule("B & (C | D)", "A", last_and_num=2)

test_rule <- list()
test_rule[[1]] <- "AMP_ATP | (ATM & ATR) | HIF1 | !(EGFR | FGFR3)"
test_rule[[2]] <- "A & ((B | C) & !(D & E))"
test_rule[[3]] <- "A & B | C"
test_rule[[4]] <- "A & B & C"
test_rule[[5]] <- "A & (B | C)"
test_rule[[6]] <- "(A | B) & (C | D)"
test_rule[[7]] <- "!(C & D) | (E & F)"
test_rule[[8]] <- "(A | B) & (C | !D) & (E | F)"
parsed_rule <- list()
for (i in c(1:length(test_rule))){
  parsed_rule[[i]] <- CellNOptR:::build_sif_table_from_rule(test_rule[[i]], "T")
}

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.