exportNetworkToVisANT: Export network data in format readable by VisANT

Description

Exports network data in a format readable and displayable by the VisANT software.

Usage

exportNetworkToVisANT(
  adjMat, 
  file = NULL, 
  weighted = TRUE, 
  threshold = 0.5, 
  maxNConnections = NULL,
  probeToGene = NULL)

Arguments

adjMat

adjacency matrix of the network to be exported.

file

character string specifying the file name of the file in which the data should be written. If not given, no file will be created. The file is in a plain text format.

weighted

logical: should the exported network by weighted?

threshold

adjacency threshold for including edges in the output.

maxNConnections

maximum number of exported adjacency edges. This can be used as another filter on the exported edges.

probeToGene

optional specification of a conversion between probe names (that label columns and rows of adjacency) and gene names (that should label nodes in the output).

Value

A data frame containing the network information suitable as input to VisANT. The same data frame is also written into a file specified by file, if given.

Details

The adjacency matrix is checked for validity. The entries can be negative, however. The adjacency matrix is expected to also have valid names or dimnames[[2]] that represent the probe names of the corresponding edges.

Whether the output is a weighted network or not, only edges whose (absolute value of) adjacency are above threshold will be included in the output. If maxNConnections is given, at most maxNConnections will be included in the output.

If probeToGene is given, it is expected to have two columns, the first one corresponding to the probe names, the second to their corresponding gene names that will be used in the output.

References

VisANT software is available from http://visant.bu.edu/.