runGquery: Run a Griffin query from an interaction graph.

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

Description

This function takes a valid gquery created with create.gquery and add.gquery methods and returns the set of boolean networks that satisfy the query.

Usage

runGquery(query, return = c("strings", "files", "iterator", "BoolNet"),
  folder.name = NULL, network.name = NULL, allow.hypothesis = F,
  allow.additional.states = F, allow.additional.cycles = F,
  allow.ambiguity = F, block.steady.a.posteriori = T,
  divide.query.by.topology = F, divide.method = c("radial",
  "sequential"), value.divide.radius = 3, value.divide.range = "1,3",
  return.network.limit = NULL)

Arguments

query	Griffin query
return	"all" return all networks as strings "files" save all networks as files in "folder.name/network.name-index.csv" "iterator" returns rjava controller "BoolNet" returns a BoolNet iterator
folder.name	folder name to save networks, default date+time
network.name	network name to save networks as files, default "net"
allow.hypothesis	activate or deactivate hypothetical regulations
allow.additional.states	allows networks with additional fixed-point attractors to those specified in the query
allow.additional.cycles	allows networks with additional cyclic attractors to those specified in the query
allow.ambiguity	allow ambiguous networks, if true ambiguous regulations may appear in the solutions
block.steady.a.posteriori	use model checking and clause learning instead of enforceing fixed-point attractors in the query
divide.query.by.topology	divide the query into multiple queries by query splitting methods
divide.method	"radial": computes centres as regulation graphs with no hypotheses and explores adding combinations of the hypothetical regulations, the number of simultaneous regulations equals the radius "sequential": sets an interval for the exploration, regulation graphs are ennumerated in a lexicographic order
value.divide.radius	(radial only) max number of simultaneous hypotheses used
value.divide.range	(sequential only) constrain in the exploration of the graphs
return.network.limit	maximum number of Boolean networks to return, if NULL there will be no limit

Examples

# Define the query
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 )
q = create.gquery.graph(inter, genes)
attr = data.frame(a=c(0,'*',0), 
                  b=c(0,1,0), 
                  c=c(0,0,1),
                  stringsAsFactors = F )
q = add.gquery.attractors(q, attr)
print( q )

# Run the query
nets = runGquery(q)
print( nets )

# Get BoolNet iterator
nets = runGquery(q, return="BoolNet")
nets
nextElem(nets)

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