https://github.com/bwlewis/tcor

Fast thresholded correlation mattices
https://github.com/bwlewis/tcor

Last synced: about 2 months ago
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Fast thresholded correlation mattices

• Host: GitHub
• URL: https://github.com/bwlewis/tcor
• Owner: bwlewis
• Created: 2015-11-28T02:17:22.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2020-08-31T11:49:28.000Z (over 4 years ago)
• Last Synced: 2024-08-13T07:12:52.830Z (5 months ago)
• Language: R
• Homepage:
• Size: 43.9 KB
• Stars: 31
• Watchers: 8
• Forks: 4
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

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• jimsghstars - bwlewis/tcor - Fast thresholded correlation mattices (R)

README

        
# 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:

```r

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.