This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms and include hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers with less than 8 bits, since a single genetic/genomic variant, like single-nucleotide polymorphism, usually occupies fewer bits than a byte. Data compression and decompression are also supported with relatively efficient random access. It is allowed to read a GDS file in parallel with multiple R processes supported by the parallel package.
The version 1.1.3 should be installed immediately, if you see the error like
Invalid Zip Deflate Stream operation 'Seek'!
Changes in v1.1.1 - 1.1.3:
Changes in v1.1.0:
* fully support big-endian systems
Xiuwen Zheng, David Levine, Jess Shen, Stephanie M. Gogarten, Cathy Laurie, Bruce S. Weir. A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics 2012; doi:10.1093/bioinformatics/bts606
Comprehensive unit testing: http://github.com/zhengxwen/unittest.gdsfmt
install_github() approach requires that you build from source, i.e.
make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.
wget --no-check-certificate https://github.com/zhengxwen/gdsfmt/tarball/master -O gdsfmt_latest.tar.gz ** Or ** curl -L https://github.com/zhengxwen/gdsfmt/tarball/master/ -o gdsfmt_latest.tar.gz ** Install ** R CMD INSTALL gdsfmt_latest.tar.gz
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.