This package was built when I was working at Xavier Estivill’s lab at Center for Genomic Regulation and it is written in collaboration with Victor Moreno and his colleagues. The R package SNPassoc contains classes and methods to help the analysis of whole genome association studies. SNPassoc utilizes S4 classes and extends haplo.stats R package to facilitate haplotype analyses. The package is useful to carry out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation and related tests (sum statistic and truncated product) are also implemented.
The package is available from CRAN, but the newest version available on CRAN is having problems with Fortran compiler. Check our GitHub account for the last updated version.
The methodology is described in:
- JR Gonzalez, L Armengol, X Sole, E Guino, JM Mercader, X Estivill, V Moreno (2007). SNPassoc: an R package to perform whole genome association studies. Bioinformatics, 23:644-5
And it has been used (among others) in:
- Real E., et al. A brain-derived neurotrophic factor (BDNF) haplotype is strongly associated with therapeutic response in obsessive-compulsive disorder. Biological Psychiatry 2009 Oct 1;66(7):674-80.
- Gratacos M., et al. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. Am J Med Genet B 2009 Sep 5;150B(6):808-16.
- Gratacos M., et al. Contribution of neurotrophic tyrosine kinase receptor type 3 (NTRK3) gene to genetic susceptibility to obsessive-compulsive hoarding. Genes Brain and Behaviour 2008 Oct;7(7):778-85
- Mercader JM., et al. Association of NTRK3 and its interaction with NGF suggest an altered cross-regulation of the neurotrophin signaling pathway in eating disorders. Hum Mol Genet. 2008 May 1;17(9):1234-44.
- de Cid R., et al. BDNF variability in opioid addicts and response to methadone treatment. Genes Brain Behav. 2008 Jul;7(5):515-22.
- Alonso P., et al. Extensive genotyping of the BDNF and NTRK2 genes define protective haplotypes against obsessive-compulsive disorder. 2008 Mar 15;63(6):619-28
- Gratacos M., et al. A brain-derived neurotrophic factor (BDNF) haplotype is associated with antidepressant treatment outcome in mood disorders. Pharmacogenomics J 8(2):101-12 (2008)