performCoexpressionAnalysis: Perform Coexpression Analysis

In Sage-Bionetworks/SageBionetworksCoex: Gene Coexpression

Description

Performs the analytic (versus graph or I/O) portion of Coexpression analysis.

Usage

performCoexpressionAnalysis(expressionData, beta = NULL, dynamicCutMethod = "tree", mergeModuleMethod = "conn")

Arguments

expressionData	A normalized matrix of gene expression data, given as a data frame with rows as samples and columns as genes/probes.
beta	Soft thresholding exponent, typically 5-6. Setting to NULL (the default) causes the function to select the optimal beta between 1 and 12.
dynamicCutMethod	"tree" or "hybrid". The former is the 'classic' approach used at Sage Bionetworks, while the latter is the default for the UCLA-WGCNA approach. The details are here: http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/Supplement.pdf
mergeModuleMethod	"conn" or "eigen". The former is the 'classic' approach used at Sage Bionetworks, in which a module's representative gene is the most highly CONNected one. The latter is the default for the UCLA-WGCNA approach, in which the representative gene is the module's EIGENvector.

Value

beta	The 'soft threshold' beta, or NULL (the default) if the function is to determine what value to use.
sftStatistics	A data frame having the statistics collected while determining beta, as produced by WGCNA::pickSoftThreshold, or NULL if beta is passed in.
dichotCor	|cc|^beta (elementwise, where 'cc' is the matrix of inter-gene Pearson correlation coefficients) but with zero diagonal.
tomDist	The toplogical overlap matrix, in the form of a distance metric.
geneTree	The gene dendrogram created from WGCNA::flashClust using 'tomDist' as the distance metric.
geneModules	A vector of module memberships, i.e. geneModules[i] is the module to which gene i belongs. "grey" is a reserved name for genes which belong to no module.
genePCTree	the dendrogram of representative vectors of each module
sampleTree	the dendrogram of samples
sampleModules	A vector of module memberships, i.e. output[i] is the module to which sample i belongs.
intraModularStatistics	A data frame of gene-wise connectivity statistics, as returned by intraModularStatistics()

Author(s)

Bruce Hoff

References

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/

Zhang, B. & Horvath, S. (2005) Statistical Applications in Genetics and Molecular Biology 4, Article 17.

Langfelder P, Zhang B, Horvath S (2007) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut library for R. Bioinformatics 2008 24(5):719-720

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/

Sage-Bionetworks/SageBionetworksCoex documentation built on May 9, 2019, 12:11 p.m.