This function creates a reusable list of network calculation arguments/options.
newNetworkOptions(
correlationOptions = newCorrelationOptions(), # Adjacency options
replaceMissingAdjacencies = TRUE,
power = 6,
networkType = c("signed hybrid", "signed", "unsigned"),
checkPower = TRUE,
# Topological overlap options
TOMType = c("signed", "unsigned", "none"),
TOMDenom = c("mean", "min"),
suppressTOMForZeroAdjacencies = FALSE,
# Internal behavior options
useInternalMatrixAlgebra = FALSE)
A list of correlation options. See newCorrelationOptions.
Logical: should missing adjacencies be replaced by zero?
Soft-thresholding power for network construction.
network type. Allowed values are (unique abbreviations of) "unsigned",
"signed", "signed hybrid". See adjacency.
Logicel: should the power be checked for sanity?
One of "none", "unsigned", "signed". If "none", adjacency
will be used for clustering. If "unsigned", the standard TOM will be used (more generally, TOM
function will receive the adjacency as input). If "signed", TOM will keep track of the sign of
correlations between neighbors.
Character string specifying the TOM variant to be used. Recognized values are
"min" giving the standard TOM described in Zhang and Horvath (2005), and "mean" in which
the min function in the denominator is replaced by mean. The "mean" may produce
better results but at this time should be considered experimental.
logical: for those components that have zero adjacency, should TOM be set to zero as well?
logical: should internal implementation of matrix multiplication be used instead of R-provided BLAS? The internal implementation is slow and this option should only be used if one suspects a bug in R-provided BLAS.
A list of class NetworkOptions.