addGqueryMutant: Add mutant with attractors to a Griffin query.

In mar-esther23/rgriffin: Gene Regulatory Interaction Formulator For Inquiring Networks

Description

Add a mutant and a set of target steady-state attractors to a Griffin query. The function takes a vector of mutant nodes, a vector of its values and a dataframe with the target attractors for the mutant where wach row corresponds to a prohibited steady state and each column corresponds to a node of the network The valid values are: 1: active 0: inactive *: non-determined

Usage

addGqueryMutant(j.query, mutant.nodes, mutant.values, df.mutant.attr)

Arguments

j.query	Griffin query
mutant.nodes	nodes whose value is fixed in the mutant
mutant.values	values of the nodes in the mutant
df.mutant.attr	dataframe with valid attractors

Value

query java query to run Griffin

Examples

# one node mutant
mutant.node = c('c')
mutant.value = c(1) 
mutant.attr = data.frame(a=c(0,1), b=c(0,0), c=c(1,1),
                         stringsAsFactors = F )
q = addGqueryMutant(q, mutant.node, mutant.value, mutant.attr)

# multiple node mutant
mutant.nodes = c('a','b')
mutant.values = c(0,0) 
mutant.attrs = data.frame(a=c(0), b=c(0), c=c('*'),
                         stringsAsFactors = F )
q = addGqueryMutant(q, mutant.nodes, mutant.values, mutant.attrs)

mar-esther23/rgriffin documentation built on May 29, 2021, 10:03 p.m.