Admixture Program

Question

[Motor Genetic]

I am new to admixture program . so After I analyze the data, I get Q values for number of K population...but it seems that program doesn't give us a predictive value that each individual belong to which population...I think in structure we can do that...does anyone has any experience on this...in another words, what would be the q cut off point for the data...thanks,

[Zev.Kronenberg]

You need to be explicit in what you are trying to do. What is the input to admixmap? What analyses are you trying to do? I'm not trying to be snarky, just trying to understand how to help you.

[Motor Genetic]

as i mentioned above, I am trying to incorporate admixture output (q matrix) results into case-control gwas association.

Answer 1

[Zev.Kronenberg]

The admixture Q-matrix is the percent membership of each individual to each K-group. Each row is an individual and each column is the k-group.

[Caddymob]

Yes, Zev has it right. To answer your question below, add the Q values as covariates to your analysis.

[Motor Genetic]

depends on number of k we are going to have 2 -3 or 5, q values for each individual. this can not be done as a single covariate.

Answer 2

[Motor Genetic]

Thanks...I know this... but how we can use this q values to separte population into two / remove outliers/ and finally perfrom admixmap analyses and case-control association test? is it adjunct to admixmap program (http://homepages.ed.ac.uk/pmckeigu/admixmap/index.html) ?

[Zev.Kronenberg]

Please use 'comment' rather than post to reply to an answer.