fast r functions for robust correlations and hierarchical clustering

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ID: 232159
2012
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Abstract
Many high-throughput biological data analyses require the calculation of large correlation matrices and/or clustering of a large number of objects. The standard R function for calculating Pearson correlation can handle calculations without missing values efficiently, but is inefficient when applied to data sets with a relatively small number of missing data. We present an implementation of Pearson correlation calculation that can lead to substantial speedup on data with relatively small number of missing entries. Further, we parallelize all calculations and thus achieve further speedup on systems where parallel processing is available. A robust correlation measure, the biweight midcorrelation, is implemented in a similar manner and provides comparable speed. The functions cor and bicor for fast Pearson and biweight midcorrelation, respectively, are part of the updated, freely available R package WGCNA.The hierarchical clustering algorithm implemented in R function hclustis an order n^3 (n is the number of clustered objects) version of a publicly available clustering algorithm (Murtagh 2012). We present the package flashClust that implements the original algorithm which in practice achieves order approximately n^2, leading to substantial time savings when clustering large data sets.
Reference Key
langfelder2012journalfast Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Peter Langfelder;Steve Horvath
Journal open geospatial data, software and standards
Year 2012
DOI
DOI not found
URL
http://www.jstatsoft.org/v46/i11/paper
Keywords
pearson correlation hierarchical clustering rstatistics

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