Understanding Epacts output

[syednaje...@gmail.com]

Dear team,

I am running an association using emmax model. I have generated a kinship file and used that for running. 

Do Epacts remove related samples while running based on the Kinship model?

I have around 6141 samples but I am getting NS|(number of samples) as 3528.

So it seems that its removing related samples.

Could you please confirm and let us know.

regards,

Najeeb 

[Hyun Min Kang]

NS is determined by the number of non-missing genotypes in your data. Is it possible that there is a lot of missingness?

Hyun.

-----------------------------------------------------
Hyun Min Kang, Ph.D.
Professor of Biostatistics
University of Michigan, Ann Arbor
Email : hmk...@umich.edu

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[Syed Najeeb Ashraf]

No, we don't have a lot of missingness,

Do epacts remove related samples while processing using kinship matrix?

To view this discussion on the web visit https://groups.google.com/d/msgid/epacts/CAPiUEki7vb32qCRzKfkE7eLBkwX7fnzeK%3DNonGCUEwkAfiRLYg%40mail.gmail.com.

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Syed Najeeb Ashraf

[Hyun Min Kang]

No, it doesn't

Perhaps your phenotypes and genotypes do not overlap very well?

Hyun.

-----------------------------------------------------
Hyun Min Kang, Ph.D.
Professor of Biostatistics
University of Michigan, Ann Arbor
Email : hmk...@umich.edu

To view this discussion on the web visit https://groups.google.com/d/msgid/epacts/CAMeMR%2BkxGkKLbBWgmgeMH1L4ErQMB4fALCHx-HYNfjU%3Dw7r_8g%40mail.gmail.com.

[Syed Najeeb Ashraf]

Thanks Dr. Hyun !!

Regards,

Najeeb 

To view this discussion on the web visit https://groups.google.com/d/msgid/epacts/CAPiUEkjVsgx0EZU5LdDCEe_2ZQ9PG_VipqspZw8gBpN8QawFBw%40mail.gmail.com.

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Syed Najeeb Ashraf

[Syed Najeeb Ashraf]

Thanks Dr,

I was able to run successfully .

Regards,

Najeeb