Package 'WGCNA' - Laboratory Web Sites - UCLA

40 exportNetworkToVisANT
exportNetworkToVisANT
Export network data in format readable by VisANT
Description
Usage
Exports network data in a format readable and displayable by the VisANT software.
exportNetworkToVisANT(
adjMat,
file = NULL,
weighted = TRUE,
threshold = 0.5,
probeToGene = NULL)
Arguments
adjMat
file
weighted
threshold
probeToGene
adjacency matrix of the network to be exported.
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.
logical: should the exported network by weighted
adjacency threshold for including edges in the output.
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).
Details
Value
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 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.
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.
Author(s)
Peter Langfelder
References
VisANT software is available from http://visant.bu.edu/.