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.
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.
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.