Calculation of the topological overlap matrix, and the corresponding dissimilarity, from a given adjacency matrix.
TOMsimilarity(
adjMat,
TOMType = "unsigned",
TOMDenom = "min",
suppressTOMForZeroAdjacencies = FALSE,
suppressNegativeTOM = FALSE,
useInternalMatrixAlgebra = FALSE,
verbose = 1,
indent = 0)
TOMdist(
adjMat,
TOMType = "unsigned",
TOMDenom = "min",
suppressTOMForZeroAdjacencies = FALSE,
suppressNegativeTOM = FALSE,
useInternalMatrixAlgebra = FALSE,
verbose = 1,
indent = 0)A matrix holding the topological overlap.
adjacency matrix, that is a square, symmetric matrix with entries between 0 and 1
(negative values are allowed if TOMType=="signed").
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.
a 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: should the results be set to zero for zero adjacencies?
Logical: should the result be set to zero when negative?
Logical: should WGCNA's own, slow, matrix multiplication be used instead of R-wide BLAS? Only useful for debugging.
integer level of verbosity. Zero means silent, higher values make the output progressively more and more verbose.
indentation for diagnostic messages. Zero means no indentation, each unit adds two spaces.
Peter Langfelder
The functions perform basically the same calculations of topological overlap. TOMdist turns the
overlap (which is a measure of similarity) into a measure of dissimilarity by subtracting it from 1.
Basic checks on the adjacency matrix are performed and missing entries are replaced by zeros.
See TOMsimilarityFromExpr for details on the various TOM types.
The underlying C code assumes that the diagonal of the adjacency matrix equals 1. If this is not the case, the diagonal of the input is set to 1 before the calculation begins.
Bin Zhang and Steve Horvath (2005) "A General Framework for Weighted Gene Co-Expression Network Analysis", Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 17
For the Nowick-type signed TOM (referred to as weighted TO, wTO, by Nowick et al.), see
Nowick K, Gernat T, Almaas E, Stubbs L. Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22358-63. doi: 10.1073/pnas.0911376106. Epub 2009 Dec 10.
or Gysi DM, Voigt A, Fragoso TM, Almaas E, Nowick K. wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool. BMC Bioinformatics. 2018 Oct 24;19(1):392. doi: 10.1186/s12859-018-2351-7.
TOMsimilarityFromExpr