Description Usage Arguments Details Value Author(s) References See Also
View source: R/blockwiseModulesC.R
Calculation of the topological overlap matrix, and the corresponding dissimilarity, from a given adjacency matrix.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | TOMsimilarity(
adjMat,
TOMType = "unsigned",
TOMDenom = "min",
suppressTOMForZeroAdjacencies = FALSE,
useInternalMatrixAlgebra = FALSE,
verbose = 1,
indent = 0)
TOMdist(
adjMat,
TOMType = "unsigned",
TOMDenom = "min",
suppressTOMForZeroAdjacencies = 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 |
a character string specifying TOM type to be calculated. One of |
TOMDenom |
a character string specifying the TOM variant to be used. Recognized values are
|
suppressTOMForZeroAdjacencies |
Logical: should TOM be set to zero for zero adjacencies? |
useInternalMatrixAlgebra |
Logical: should WGCNA's own, slow, matrix multiplication be used instead of R-wide 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.
If TOMType = "unsigned"
, entries of the adjacency matrix are required to lie between 0 and 1;
for TOMType = "signed"
they can be between -1 and 1. In both cases the resulting TOM entries, as
well as the corresponding dissimilarities, lie between 0 and 1.
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 Co-Expression Network Analysis", Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 17
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