Analyzing SNP data

I hope to be starting on SNP data analyses in the earnest today. I am attending a workshop on data-cleaning and quality control of genetic data this morning. I then have a meeting to see what data I can get for analyses.

The first step?

Chucked out the evil spawn of linux known as Fedora and installed Ubuntu. And what a difference in display quality! Now for the brass tacks

1. Installed PLINK 1.07-1. Ubuntu Software Center > PLINK
   
2. Can whatever PLINK does be done using R alone?
   

The baseline variable shipped along with the SNPs include:

1. StudyID
   
2. Case_Control
   
3. age {at reference date?}
   
4. A5 {Hispanic ethnicity?}
   
5. A7 {Highest grade of school completed}
   
6. D1 {Age at menarche}
   
7. menopause {Menopausal status}
   
8. agemenopause {Age at menopause}
   
9. bmi
   
10. tanita_bmi {Tanita scale Body Mass Index (kg/m^2)}
    
11. bmi_self
    
12. agefirstbirth {Age at first live birth}
    
13. birthcount {Number of live births}
    
14. agefirstpreg {Age at first full-term pregnancy}
    
15. pregnum {Number of full-term pregancies}
    

breastfeed breastfeedmonths G8 F1 waist hip waisthip race eversmok calories carbo fat protein fiber fibh2o fibinso F5 fhbc Hmm what are these...

1. phenotype
   
2. state
   
3. control_source
   

Outcomes

1. ERStatus
   
2. PRStatus
   
3. her2status
   
4. TumorGrade
   
5. TumorStage
   
6. invasive
   
7. tumor_subtype
   
8. triplenegative
   
9. Eurpr