modOr: Module-oriented multiple module membership clustering

Description Usage Arguments References

View source: R/modOr.R

Description

Allows for a module-oriented, as opposed to a gene-oriented, output format of multiple module clustering. The analysis of these two methods are extremely similar, but the outputs are useful for very different types of analyses.

Usage

1
modOr(threshold, kME, cap)

Arguments

threshold

A number between zero and one that serves as a cutoff of how well a Module must correlate with a certain module before it is considered part of that module in the analysis. A typical value is around 0.75 (the default), with more stringent analyses occuring around 0.90.

kME

The module eigenvalues outputted by WGCNA's 'blockwiseModules' or 'moduleEigenModules' functions. This is a required input.

cap

Sets a maximum number of modules to which a gene may be assigned. The default is five.

References

Langfelder P and Horvath S, WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008, 9:559 doi:10.1186/1471-2105-9-559

Peter Langfelder, Steve Horvath (2012). Fast R Functions for Robust Correlations and Hierarchical Clustering. Journal of Statistical Software, 46(11), 1-17. URL http://www.jstatsoft.org/v46/i11/.


jsieker/MultiMod documentation built on Jan. 9, 2018, 10:14 a.m.