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", "signed Nowick", "unsigned", "none",
"signed 2", "signed Nowick 2", "unsigned 2"),
TOMDenom = c("mean", "min"),
suppressTOMForZeroAdjacencies = FALSE,
suppressNegativeTOM = 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", "signed Nowick",
"unsigned 2", "signed 2" and "signed Nowick 2". If "none", adjacency
will be used for clustering. See TOMsimilarityFromExpr for details.
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 the result be set to zero when negative? Negative TOM values can occur when
TOMType is "signed Nowick".
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.