Using Mata to import Illumina SNP chip data for genome-wide association studies
AbstractModern genetic genome-wide association studies typically rely on single nucleotide polymorphism (SNP) chip technology to determine hundreds of thousands of genotypes for an individual sample. Once these genotypes are ascertained, each SNP alone or in combination is tested for association outcomes of interest such as disease status or severity. Project Heartbeat! was a longitudinal study conducted in the 1990s that explored changes in lipids and hormones and morphological changes in children from 8 to 18 years of age. A genome-wide association study is currently being conducted to look for SNPs that are associated with these developmental changes. While there are specialty programs available for the analysis of hundreds of thousands of SNPs, they are not capable of modeling longitudinal data. Stata is well equipped for modeling longitudinal data but cannot load hundreds of thousands of variables into memory simultaneously. This talk will briefly describe the use of Mata to import hundreds of thousands of SNPs from the Illumina SNP chip platform and how to load those data into Stata for longitudinal modeling.
Download InfoIf you experience problems downloading a file, check if you have the proper application to view it first. In case of further problems read the IDEAS help page. Note that these files are not on the IDEAS site. Please be patient as the files may be large.
Bibliographic InfoPaper provided by Stata Users Group in its series United Kingdom Stata Users' Group Meetings 2011 with number 16.
Date of creation: 26 Sep 2011
Date of revision:
This paper has been announced in the following NEP Reports:
- NEP-ALL-2011-10-09 (All new papers)
You can help add them by filling out this form.
reading list or among the top items on IDEAS.Access and download statisticsgeneral information about how to correct material in RePEc.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: (Christopher F Baum).
If references are entirely missing, you can add them using this form.