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README.md

tcor

An R package for fast and memory-efficient computation of thresholded correlation matrices

A preprint of the companion note is available from http://arxiv.org/abs/1512.07246.

Installation

The package depends on the irlba (https://cran.r-project.org/web/packages/irlba/) and foreach (https://cran.r-project.org/web/packages/foreach/) packages, each available on CRAN. You can install tcor using the devtools package (https://cran.r-project.org/web/packages/devtools/) with:

devtools::install_github("bwlewis/tcor")

The algorithm can optionally make use of foreach package "back-ends" to run in parallel Many are available, including doMC, doParallel, and doRedis. See the CRAN high performance computing task view for more info https://cran.r-project.org/web/views/HighPerformanceComputing.html.

Example

See the vignette https://github.com/bwlewis/tcor/blob/master/vignettes/brca.Rmd for an example that uses tcor to compute the most correlated gene expression vectors from TCGA RNASeq data.

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