runGquery: Run a Griffin query from an interaction graph.

Description Usage Arguments Examples

View source: R/runQuery.R

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

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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

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# 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 Nov. 21, 2020, 7:42 p.m.