# TOMsimilarity: Topological overlap matrix similarity and dissimilarity In WGCNA: Weighted Correlation Network Analysis

## Description

Calculation of the topological overlap matrix, and the corresponding dissimilarity, from a given adjacency matrix.

## Usage

 ``` 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) ```

## Arguments

 `adjMat` adjacency matrix, that is a square, symmetric matrix with entries between 0 and 1 (negative values are allowed if `TOMType=="signed"`). `TOMType` a character string specifying TOM type to be calculated. One of `"unsigned"`, `"signed"`. If `"unsigned"`, the standard TOM will be used (more generally, TOM function will receive the adjacency as input). If `"signed"`, TOM will keep track of the sign of the adjacency between neighbors. `TOMDenom` 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.
 `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.

## Details

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.

## Value

A matrix holding the topological overlap.

Peter Langfelder

## References

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

`TOMsimilarityFromExpr`

WGCNA documentation built on March 18, 2018, 2:28 p.m.