net_query: Network querying method based on conditional random fields

Description Usage Arguments Details References Examples

View source: R/net_query.R

Description

Find the best matching subnetworks from a large target network for small query networks based on the conditional random fields (CRF) model.

Usage

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net_query(query.net, target.net, node.sim, query.type = 4, delta.d = 1e-10,
  delta.c = 0.5, delta.e = 1, delta.s = 1, output = "result.txt")

net_query_batch(query.nets, target.net, node.sim, query.type = 4,
  delta.d = 1e-10, delta.c = 0.5, delta.e = 1, delta.s = 1,
  output = "result.txt")

Arguments

query.net

The input file name of the query network.

target.net

The input file name of the target network.

node.sim

The input file name of the node similarity scores between the query network and the target network.

query.type

The querying network type: 1 - general, 2 - chain, 3 - tree, 4 - heuristic.

delta.d

The parameter delta.d is a parameter for deletions.

delta.c

The parameter delta.c is a parameter for consecutive deletions.

delta.e

The parameter delta.e is a parameter for single deletion.

delta.s

The parameter delta.s is a parameter for insertions.

output

The suffix of output file name.

query.nets

The vector of input file names of the query networks.

Details

This is an approach for network querying problem based on conditional random field (CRF) model which can handle both undirected and directed networks, acyclic and cyclic networks, and any number of insertions/deletions.

When querying several networks in the same target network, net_query_batch will save much time.

References

Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang. An Efficient Network Querying Method Based on Conditional Random Fields. Bioinformatics, 27(22):3173-3178, 2011.

Examples

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## Not run: 
library(Corbi)

## An example: "querynet.txt", "targetnet.txt", "nodesim.txt" are
## three input files in the working directory
net_query("querynet.txt", "targetnet.txt", "nodesim.txt", query.type=3)

## End(Not run)


## Not run: 
## Batch example
net_query_batch(c("querynet.txt", "querynet2.txt"),
  "targetnet.txt", "nodesim.txt", query.type=3)

## End(Not run)

wulingyun/Corbi documentation built on May 28, 2017, 6:37 a.m.