View source: R/blockwiseModulesC.R
TOMsimilarity  R Documentation 
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)
adjMat 
adjacency matrix, that is a square, symmetric matrix with entries between 0 and 1
(negative values are allowed if 
TOMType 
one of 
TOMDenom 
a character string specifying the TOM variant to be used. Recognized values are

suppressTOMForZeroAdjacencies 
Logical: should the results be set to zero for zero adjacencies? 
suppressNegativeTOM 
Logical: should the result be set to zero when negative? 
useInternalMatrixAlgebra 
Logical: should WGCNA's own, slow, matrix multiplication be used instead of Rwide BLAS? Only useful for debugging. 
verbose 
integer level of verbosity. Zero means silent, higher values make the output progressively more and more verbose. 
indent 
indentation for diagnostic messages. Zero means no indentation, each unit adds two spaces. 
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.
A matrix holding the topological overlap.
Peter Langfelder
Bin Zhang and Steve Horvath (2005) "A General Framework for Weighted Gene CoExpression Network Analysis", Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 17
For the Nowicktype 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):2235863. 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/s1285901823517.
TOMsimilarityFromExpr
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