FlashPCA 2.0

FlashPCA2

Major changes

• v2.0 replaces the randomised PCA algorithm of v1 with Spectra's IRAM, making it faster and more stable, while using less memory.
• Most of the commandline functionality is also available within R (using the standalone package flashpcaR).

Files in this release

• flashpcaR, standalone R package
  • flashpcaR_2.0.tar.gz: flashpcaR source package for Linux
  • flashpcaR_2.0.tgz: flashpcaR binary package for Mac Intel 64-bit
  • flashpcaR_2.0.zip: flashpcaR binary package for Windows
• flashpca (command line tool)
  • flashpca_x86-64.gz: statically-linked binary for Linux (>=2.6.15), compiled with gcc 5.1.1, Eigen 3.3.0, boost 1.55, with march=core2
  • flashpca-mac-intel: dynamically-linked binary for Mac Intel 64-bit
• Source for flashpca and flashpcaR (compiling for your target system is recommended for best performance)
  • flashpca_2.0.tar.gz

flashpca v1.2.6

Major changes:

• Small updates to sparse canonical correlation code (flashpcaR::scca)

Files in this release:

• flashpcaR (R package)
  • flashpcaR_1.2.6.tgz: flashpcaR R binary package for Mac 64-bit (compiled on 10.11.3 with clang-700.1.81)
  • flashpcaR_1.2.6.zip: flashpcaR R binary package for Windows (compiled on http://win-builder.r-project.org)
  • flashpcaR_1.2.6.tar.gz: flashpcaR source package, for Linux (requires compiling)
• flashpca (command line tool)
  • flashpca_x86-64.gz: static binary for 64-bit Linux (>=2.6.15), compiled with gcc 5.1.1, Eigen 3.2.8, Boost 1.55.0, with march=core2

flashpca v1.2.5

Major changes

• Fixed bug in reading PLINK bed files, allowing analysis of larger datasets (essentially limited by available RAM). Has been tested on Linux with datasets with ~160,000 individuals and ~139,000 SNPs (requiring 166GB RAM using --mem low).
• Clean-ups and better documentation for flashpcaR.

Files in this release:

flashpcaR (R package)

• flashpcaR_1.2.5.tgz: flashpcaR R binary package for Mac 64-bit (compiled on 10.10.5 with gcc 4.9)
• flashpcaR_1.2.5.zip: flashpcaR R binary package for Windows (compiled on http://win-builder.r-project.org)
• flashpcaR_1.2.5.tar.gz: flashpcaR source package, for Linux (requires compiling)

flashpca (command line tool)

• flashpca_x86-64: static binary for 64-bit Linux (>=2.6.15), compiled with gcc 5.1.1, Eigen 3.2.5, Boost 1.55.0, with march=core2

Precompiled Windows binaries for flashpcaR 1.1.2

Precompiled Windows binaries of flashpcaR.

In R, you can install using by specifying the path you downloaded it to, e.g.:
install.packages("C:/Users/abrahamg/Downloads/flashpcaR_1.0.zip", repos = NULL)

Note: this version does not support OpenMP multi-threading.