vectorTOM: Topological overlap for a subset of the whole set of genes

In WGCNA: Weighted Correlation Network Analysis

Topological overlap for a subset of the whole set of genes

Description

This function calculates topological overlap of a small set of vectors with respect to a whole data set.

Usage

vectorTOM(
  datExpr, 
  vect, 
  subtract1 = FALSE, 
  blockSize = 2000, 
  corFnc = "cor", corOptions = "use = 'p'", 
  networkType = "unsigned", 
  power = 6, 
  verbose = 1, indent = 0)

Arguments

datExpr	a data frame containing the expression data of the whole set, with rows corresponding to samples and columns to genes.
vect	a single vector or a matrix-like object containing vectors whose topological overlap is to be calculated.
subtract1	logical: should calculation be corrected for self-correlation? Set this to TRUE if vect contains a subset of datExpr.
blockSize	maximum block size for correlation calculations. Only important if vect contains a large number of columns.
corFnc	character string giving the correlation function to be used for the adjacency calculation. Recommended choices are "cor" and "bicor", but other functions can be used as well.
corOptions	character string giving further options to be passed to the correlation function.
networkType	character string giving network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See adjacency.
power	soft-thresholding power for network construction.
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

Topological overlap can be viewed as the normalized count of shared neighbors encoded in an adjacency matrix. In this case, the adjacency matrix is calculated between the columns of vect and datExpr and the topological overlap of vectors in vect measures the number of shared neighbors in datExpr that vectors of vect share.

Value

A matrix of dimensions n*n, where n is the number of columns in vect.

Author(s)

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

See Also

TOMsimilarity for standard calculation of topological overlap.

WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.