GWASTools-package {GWASTools} | R Documentation

## Tools for Genome Wide Association Studies

### Description

This package contains tools for facilitating cleaning (quality control and quality assurance) and analysis of GWAS data.

### Details

GWASTools provides a set of classes for storing data and annotation from Genome Wide Association studies, and a set of functions for data cleaning and analysis that operate on those classes.

Genotype and intensity data are stored in external files (GDS or NetCDF), so it is possible to analyze data sets that are too large to be contained in memory. The `GenotypeReader` class and `IntensityReader` class unions provide a common interface for GDS and NetCDF files.

Two sets of classes for annotation are provided. `SnpAnnotationDataFrame` and `ScanAnnotationDataFrame` extend `AnnotatedDataFrame` and provide in-memory containers for SNP and scan annotation and metadata. `SnpAnnotationSQLite` and `ScanAnnotationSQLite` provide interfaces to SNP and scan annotation and metadata stored in SQLite databases.

The `GenotypeData` and `IntensityData` classes combine genotype or intensity data with SNP and scan annotation, ensuring that the data in the NetCDF files is consistent with annotation through unique SNP and scan IDs. A majority of the functions in the GWASTools package take `GenotypeData` and/or `IntensityData` objects as arguments.

### Author(s)

Stephanie M. Gogarten, Cathy Laurie, Tushar Bhangale, Matthew P. Conomos, Cecelia Laurie, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar, Adrienne Stilp

Maintainer: Stephanie M. Gogarten sdmorris@u.washington.edu

### References

Laurie, C. C., Doheny, K. F., Mirel, D. B., Pugh, E. W., Bierut, L. J., Bhangale, T., Boehm, F., Caporaso, N. E., Cornelis, M. C., Edenberg, H. J., Gabriel, S. B., Harris, E. L., Hu, F. B., Jacobs, K. B., Kraft, P., Landi, M. T., Lumley, T., Manolio, T. A., McHugh, C., Painter, I., Paschall, J., Rice, J. P., Rice, K. M., Zheng, X., and Weir, B. S., for the GENEVA Investigators (2010), Quality control and quality assurance in genotypic data for genome-wide association studies. Genetic Epidemiology, 34: 591-602. doi: 10.1002/gepi.20516

[Package GWASTools version 1.40.0 Index]