Question: Admixture Program
0
gravatar for Motor Genetic
7.1 years ago by
Motor Genetic100
Motor Genetic100 wrote:

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,

population genetics • 4.1k views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 7.1 years ago by Motor Genetic100

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.

ADD REPLYlink written 7.1 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 7.1 years ago by Motor Genetic100
1
gravatar for Zev.Kronenberg
7.1 years ago by
United States
Zev.Kronenberg11k wrote:

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.

ADD COMMENTlink written 7.1 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 7.1 years ago by Caddymob950

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.

ADD REPLYlink written 7.1 years ago by Motor Genetic100
0
gravatar for Motor Genetic
7.1 years ago by
Motor Genetic100
Motor Genetic100 wrote:

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) ?

ADD COMMENTlink written 7.1 years ago by Motor Genetic100
1

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

ADD REPLYlink written 7.1 years ago by Zev.Kronenberg11k
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