Export network data in format readable by VisANT
Exports network data in a format readable and displayable by the VisANT software.
exportNetworkToVisANT( adjMat, file = NULL, weighted = TRUE, threshold = 0.5, maxNConnections = NULL, probeToGene = NULL)
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 |
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.
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.
Peter Langfelder
VisANT software is available from http://www.visantnet.org/visantnet.html/.
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