Answers.Body: <p>Interesting question I would recommend the effective population size <span class="math-container">$N_{e}$</span>,  and error bars around this. Ne can be calculated via <span class="math-container">$F_{st}$</span> and is perhaps the most important parameter to determine the genetic population size.</p>
  <p>Under the Fisher definition <span class="math-container">$N_{e}$</span> is the number of breeding individuals in the population.</p>
  <p>The central issue with the approach you are suggesting is that population size does not equate to genetic population size. Thus the population could be huge, but if it is genetically homogeneous it will appear very small. In contrast the number of individuals could be very small, but the genetic variation between between them very large so <span class="math-container">$N_{e}$</span> would be huge.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-05T12:35:22.200Z
Answers.Text: Appreciated promt response.            Actually, our population  is humogeneous, and have very low sample size.  I wonder, is there any (genetics related) software where i can play around Ne and Fst?
Answers.UserDisplayName: user2808642
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-05T12:50:45.047Z
Answers.Text: Usual suspects Arlequin etc.. because you have low diversity the traditional stuff will work
Answers.UserDisplayName: M__
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Answers.CreationDate: 2020-08-05T12:29:43.440Z
Answers.LastActivityDate: 2020-08-05T12:29:43.440Z
Answers.UserDisplayName: M__
Body: <p>I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease.</p>
  <p>I wonder, does anyone has came across this? Really appreciate any suggestion or any tool/software which can answer this?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-05T14:18:32.107Z
Comments.Text: Might be worth having a look at this website: http://csg.sph.umich.edu/abecasis/gas_power_calculator/
Comments.UserDisplayName: user438383
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Comments.CreationDate: 2020-08-05T14:22:25.940Z
Comments.Text: thanks, but this if for case/control only. Our study is NOT case/control. Any other suggestion?
Comments.UserDisplayName: user2808642
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Comments.CreationDate: 2020-08-05T14:24:39.067Z
Comments.Text: OK - could you edit your question to include some more details about the study you are planning (i.e. quantitative/discrete traits, species, intended outcome etc) and it might make it easier for people to give a good answer to your question. cheers.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-05T14:34:59.467Z
Comments.Text: I just Edited the question.
Comments.UserDisplayName: user2808642
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-05T21:45:06.257Z
Comments.Text: Do you mean continuous? If it's discrete and there are only two conditions, then the power calculations should be the same as for a case/control study.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-06T08:06:31.957Z
Comments.Text: @gringer yes I was also confused by this. what is the actual trait you are looking at?
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-06T09:12:20.403Z
Comments.Text: Sorry for confusing, its a trait in young girls about their early stage in sexual maturation that happens in some higher primates and in humans, typically peaks at around 20 years of age, and is eventually involved in the development of pubic hair, body odor etc.
Comments.UserDisplayName: user2808642
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-06T14:02:27.933Z
Comments.Text: OK, so the trait is a continuous variable? In this case, it seems like it can be a 'time' value, like 5 years, 6 years, 5.1 years etc?
Comments.UserDisplayName: user438383
Tags: <bioconductor><gwas><human-genome><phylogenetics><molecular-genetics>
Title: Power calculation for GWAS/EWAS
ThreadText: # Power calculation for GWAS/EWAS
  
  (Asked by: username_0 on 2020-08-05)
  
  I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease.
  
  I wonder, does anyone has came across this? Really appreciate any suggestion or any tool/software which can answer this?
  
  **Tags:** bioconductor, gwas, human-genome, phylogenetics, molecular-genetics
  
  > **Comments:**
  > **username_1**: Might be worth having a look at this website: http://csg.sph.umich.edu/abecasis/gas_power_calculator/  
  > **username_0**: thanks, but this if for case/control only. Our study is NOT case/control. Any other suggestion?  
  > **username_1**: OK - could you edit your question to include some more details about the study you are planning (i.e. quantitative/discrete traits, species, intended outcome etc) and it might make it easier for people to give a good answer to your question. cheers.  
  > **username_0**: I just Edited the question.  
  > **username_2**: Do you mean continuous? If it's discrete and there are only two conditions, then the power calculations should be the same as for a case/control study.  
  > **username_1**: @username_2 yes I was also confused by this. what is the actual trait you are looking at?  
  > **username_0**: Sorry for confusing, its a trait in young girls about their early stage in sexual maturation that happens in some higher primates and in humans, typically peaks at around 20 years of age, and is eventually involved in the development of pubic hair, body odor etc.  
  > **username_1**: OK, so the trait is a continuous variable? In this case, it seems like it can be a 'time' value, like 5 years, 6 years, 5.1 years etc?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2020-08-05. Score: 1
  
  Interesting question I would recommend the effective population size $N\_{e}$, and error bars around this. Ne can be calculated via $F\_{st}$ and is perhaps the most important parameter to determine the genetic population size.
  
  Under the Fisher definition $N\_{e}$ is the number of breeding individuals in the population.
  
  The central issue with the approach you are suggesting is that population size does not equate to genetic population size. Thus the population could be huge, but if it is genetically homogeneous it will appear very small. In contrast the number of individuals could be very small, but the genetic variation between between them very large so $N\_{e}$ would be huge.
  
  > **Comments:**
  > **username_0**: Appreciated promt response.            Actually, our population  is humogeneous, and have very low sample size.  I wonder, is there any (genetics related) software where i can play around Ne and Fst?  
  > **username_3**: Usual suspects Arlequin etc.. because you have low diversity the traditional stuff will work  
  
  ---
  
  