Description Usage Arguments Details Value Author(s) References See Also
View source: R/blockwiseModulesC.R
Calculation of the topological overlap matrix from given expression data.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  TOMsimilarityFromExpr(
datExpr,
weights = NULL,
corType = "pearson",
networkType = "unsigned",
power = 6,
TOMType = "signed",
TOMDenom = "min",
maxPOutliers = 1,
quickCor = 0,
pearsonFallback = "individual",
cosineCorrelation = FALSE,
replaceMissingAdjacencies = FALSE,
suppressTOMForZeroAdjacencies = FALSE,
suppressNegativeTOM = FALSE,
useInternalMatrixAlgebra = FALSE,
nThreads = 0,
verbose = 1, indent = 0)

datExpr 
expression data. A data frame in which columns are genes and rows ar samples. NAs are allowed, but not too many. 
weights 
optional observation weights for 
corType 
character string specifying the correlation to be used. Allowed values are (unique
abbreviations of) 
networkType 
network type. Allowed values are (unique abbreviations of) 
power 
softthresholding power for netwoek construction. 
TOMType 
one of 
TOMDenom 
a character string specifying the TOM variant to be used. Recognized values are

maxPOutliers 
only used for 
quickCor 
real number between 0 and 1 that controls the handling of missing data in the calculation of correlations. See details. 
pearsonFallback 
Specifies whether the bicor calculation, if used, should revert to Pearson when median
absolute deviation (mad) is zero. Recongnized values are (abbreviations of)

cosineCorrelation 
logical: should the cosine version of the correlation calculation be used? The cosine calculation differs from the standard one in that it does not subtract the mean. 
replaceMissingAdjacencies 
logical: should missing values in the calculation of adjacency be replaced by 0? 
suppressTOMForZeroAdjacencies 
Logical: should the result 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. 
nThreads 
nonnegative integer specifying the number of parallel threads to be used by certain parts of correlation calculations. This option only has an effect on systems on which a POSIX thread library is available (which currently includes Linux and Mac OSX, but excludes Windows). If zero, the number of online processors will be used if it can be determined dynamically, otherwise correlation calculations will use 2 threads. 
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. 
Several alternate definitions of topological overlap are available. The oldest version is now called "unsigned"; in this version, all adjacencies are assumed to be nonnegative and the topological overlap of nodes i,j is given by
TOM[i,j] = ( a[i,j] + ∑ a[i,k] a[k,j] )/(f(k[i], k[j]) + 1  a[i,j]),
where the sum is over k not equal to either i or j, the function f in the denominator can be
either min or mean (goverened by argument TOMDenom
), and k[i] = sum a[i,j] is
the connectivity of node i. The signed versions assume that the adjacency matrix was obtained from an underlying
correlation matrix, and the element a[i,j] carries the sign of the underlying correlation of the two
vectors. (Within WGCNA, this can really only apply to the unsigned adjacency since signed adjacencies are (essentially)
zero when the underlying correlation is negative.) The signed and signed Nowick versions are similar to the above unsigned
version, differing only in absolute
values placed in the expression: the signed Nowick expression is
TOM[i,j] = ( a[i,j] + ∑ a[i,k] a[k,j] )/(f(k[i], k[j]) + 1  a[i,j]).
This TOM lies between 1 and 1, and typically is negative when the underlying adjacency is negative. The signed TOM is simply the absolute value of the signed Nowick TOM and is hence always nonnegative. For nonnegative adjacencies, all 3 version give the same result.
A brief note on terminology: the original article by Nowick et al use the name "weighted TO" or wTO; since all of the topological overlap versions calculated in this function are weighted, we use the name signed to indicate that this TOM keeps track of the sign of the underlying correlation.
The "2" versions of all 3 adjacency types have a somewhat different form in which the adjacency and the product are normalized separately. Thus, the "unsigned 2" version is
TOM2[i,j] = 0.5 ( a[i,j] + ∑ a[i,k] a[k,j] /(f(k[i], k[j])  a[i,j])).
At present the relative weight of the adjacency and the normalized product term are equal and fixed; in the future a userspecified or automatically determined weight may be implemented. The "signed Nowick 2" and "signed 2" are defined analogously to their original versions. The adjacency is assumed to be signed, and the expression for "signed Nowick 2" TOM is
TOM2[i,j] = 0.5 ( a[i,j] + ∑ a[i,k] a[k,j] /(f(k[i], k[j])  a[i,j])).
Analogously to "signed" TOM, "signed 2" differs from "signed Nowick 2" TOM only in taking the absolute value of the result.
At present the "2" versions should all be considered experimental and are subject to change.
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
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