GWAS2 : GWAA; New Data Generation

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Name
GWAS2
Title
GWAA; New Data Generation
Verified
No
Author
Sara Nunez, Tu Dao
Uploaded By
nunezsa
Date Created
2015-06-29
Last Modified
2015-09-16
Download Count
24
View Count
2416
Current Version
2.0
File Size
Description
New data generation is the second step involved in many GWAS analyses. It involves generating principal components to be included in a predictive model as well as imputing missing SNPs to increase power. Work saved from module 1 in this series (entitled GWAS1) is utilizing in these labs. The first lab in this module walks students through how to compute principal components (PCs) to be used in a model of association. This is done to adjust for population substructure in the data. The second lab demonstrates one way that missing SNPs can be imputed using a reference panel. In our example, we impute SNPs that are present in the 1000 Genomes Project data on chromosome 16. In practice, this can be done in R but is more commonly done using external tools.



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