subsetTOM: Topological overlap for a subset of a whole set of genes

Description

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

Usage

subsetTOM(
  datExpr, 
  subset,
  corFnc = "cor", corOptions = "use = 'p'", 
  weights = NULL,  
  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.

subset

a single logical or numeric vector giving the indices of the nodes for which the TOM is to be calculated.

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.

weights

optional observation weights for datExpr to be used in correlation calculation. A matrix of the same dimensions as datExpr, containing non-negative weights. Only used with Pearson correlation.

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.

Value

A matrix of dimensions n*n, where n is the number of entries selected by block.

Details

This function is designed to calculated topological overlaps of small subsets of large expression data sets, for example in individual modules.

References