ATOM: Association Test via Optimally-weighted Markers

The program is written in R (www.r-project.org). This package has four files. The analysis functions are in ATOM.r. The other three files provide example data and code for running ATOM.

To run ATOM, you need to prepare a reference data set for the region of interest. Our example data set was extracted from the HapMap. As shown in the example code, only the genotype data in the reference file are used.

Please see the file ATOM.r for detailed explanations of the arguments of ATOM().

The paper that describes the method is:

Li M, Wang K, Grant SF, Hakonarson H, Li C (2009) ATOM: A powerful gene-based association test by combining optimally weighted markers. Bioinformatics 25:497-503 (PMID: 19074959) (paper)