Download

Download the latest R-package builds

The R-packages are not system specific, but a *NIX environment is recommended. Please verify the integrity of your downloads using the provided md5 or sha2 hashes.

Latest build enabling all 11 population codes (requires IRanges: 1.14, R ≥ 2.15.0)

Older build enabling all 11 population codes (requires IRanges: 1.12, R 2.14)

Previous build (requires Bioconductor 2.10, R 2.14)

Older versions (compatible with Bioconductor 2.9, R 2.13)

Download data

To keep the package size relatively small, it contains only demo data for human chromosome 12. To perform your own computation using binning based on the International HapMap project's LD-data, the full LD-dataset is required. It contains the LD data for all 11 HapMap populations and is converted from the original data in text format, based on HapMap Release 27. You can download the LD-data here:

Note: If you have already downloaded this file, you do not need to download it again to use all 11 HapMap population codes. The data is already contained in the file you have.
  • Alternatively, we have generated LD data (r2 >= 0.2) from the 1000 genomes pilot 1 data for the EUR population code only: LD1kgEUR.h5 (~2.2 GB)
If you want to generate LD files yourself, the code and instructions for doing this is available on GitHub. (using makefiles, it is not very streamlined)

Updated Annotation Data

There was an omission in the previous version of the annotation data. 390 Ensembl entries were omitted because they did not successfully convert back to NCBI build 36 coordinates, due to splits or deletions in their sequence. While a large majority of these were predicted sequences or unknown elements, some known genes were also omitted. A list of the missing 390 entries is here. This error has been subsequently corrected to the best of our ability. The updated Ensembl 66 datafile is now available. We ask you to not use the old annotation file and to re-run any calculations based on it; please see the README for details.

To use LDsnpR with the latest genome annotation, we have downloaded all ENSEMBL 66 genes and converted the coordinates back to NCBI bld36, please see the README for details. Note that all SNP and gene positions must be consistently provided in NCBI bld36 coordinates for now. The EnsEMBL 66 (March 2012) gene annotation can be downloaded from here:

The EnsEMBL 54 (May 2009) gene annotation can also be obtained from here:

The original data used in this study was provided with kind permission. To obtain these data-sets, please contact the owners of the data directly.

Getting access to the source code

The source code of the R-packages is available via anonymous read-only access using the subversion revision control system. at

Using the command-line svn client, you can checkout the full source tree into your working directory in the following way:
$ svn co http://www.ii.uib.no/svn/eSysBio/Rpackages/hdf5mod/
$ svn co http://www.ii.uib.no/svn/eSysBio/Rpackages/LDsnpR/
To keep your source tree up to date, change working directory to your svn directory and run:
$ svn update hdf5mod
$ svn update LDsnpR

If you wish to contribute code, please contact the authors.