Description Usage Arguments Value Author(s) See Also
This function creates a reusable list of network calculation arguments/options.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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)
|
correlationOptions |
A list of correlation options. See |
replaceMissingAdjacencies |
Logical: should missing adjacencies be replaced by zero? |
power |
Soft-thresholding power for network construction. |
networkType |
network type. Allowed values are (unique abbreviations of) |
checkPower |
Logicel: should the power be checked for sanity? |
TOMType |
One of |
TOMDenom |
Character string specifying the TOM variant to be used. Recognized values are
|
suppressTOMForZeroAdjacencies |
logical: for those components that have zero adjacency, should TOM be set to zero as well? |
useInternalMatrixAlgebra |
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
.
Peter Langfelder
codenewCorrelationOptions
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