createGqueryGraph: Create a Griffin query.

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

Description

This function takes an interaction regulatory graph and creates a griffin query.

Usage

createGqueryGraph(df.graph, nodes)

Arguments

df.graph	dataframe with source nodes, target nodes and the type of interactions
nodes	vector with all node names

Details

The graph must include: source, target and type of interaction Valid types of interctions are: false: Contradiction MA: Mandatory, ambiguous MPU (or +): Mandatory, positive, unambiguous MPPA: Mandatory, positive, possibly ambiguous MNU (or -): Mandatory, negative, unambiguous MNPA: Mandatory, negative, possibly ambiguous MUSU: Mandatory, unknown sign, unambiguous MUSPA: Mandatory, unknown sign, possibly ambiguous NR: No regulation OA: Optional, ambiguous OPU: Optional, positive, unambiguous OPPA: Optional, positive, possibly ambiguous ONU: Optional, negative, unambiguous ONPA: Optional, negative, possibly ambiguous OUSU: Optional, unknown sign, unambiguous true: Tautology

Value

query java query to run Griffin

Examples

> genes = c('a','b','c')
> inter = data.frame(source=c('a','b','b','c','c'), 
                     target=c('b','b','c','b','c'), 
                     type=c('+','+','+','-','+'),
                     stringsAsFactors = F )
> createGqueryGraph(inter, genes)

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