compCorrGraph: A function to compute a correlation based graph from Gene
Expression Data
Description
Given a set of gene expression data (an instance of the
ExpressionSet class) this function computes a graph based on
correlations between the probes.
Usage
compCorrGraph(eSet, k = 1, tau = 0.6)
Arguments
eSet
An instance of the ExpressionSet class.
k
The power to raise the correlations to.
tau
The lower cutoff for absolute correlations.
Value
An instance of the graph class. With edges and edge weights
determined by applying the algorithm described previously.
Details
Zhou et al. describe a method of computing a graph between probes
(genes) based on estimated correlations between probes. This function
implements some of their methods.
Pearson correlations between probes are computed and then these are
raised to the power k. Any of the resulting estimates that are
less than tau in absolute value are set to zero.
References
Zhou et al., Transitive functional annotation by
shortest-path analysis of gene expression data.