<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>

CC BY-SA 4.0
2020-08-05T12:35:22.200Z
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?
user2808642
CC BY-SA 4.0
2020-08-05T12:50:45.047Z
Usual suspects Arlequin etc.. because you have low diversity the traditional stuff will work
M__
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2020-08-05T12:29:43.440Z
2020-08-05T12:29:43.440Z
M__
<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>

CC BY-SA 4.0
2020-08-05T14:18:32.107Z
Might be worth having a look at this website: http://csg.sph.umich.edu/abecasis/gas_power_calculator/
user438383
CC BY-SA 4.0
2020-08-05T14:22:25.940Z
thanks, but this if for case/control only. Our study is NOT case/control. Any other suggestion?
user2808642
CC BY-SA 4.0
2020-08-05T14:24:39.067Z
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.
user438383
CC BY-SA 4.0
2020-08-05T14:34:59.467Z
I just Edited the question.
user2808642
CC BY-SA 4.0
2020-08-05T21:45:06.257Z
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.
gringer
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2020-08-06T08:06:31.957Z
@gringer yes I was also confused by this. what is the actual trait you are looking at?
user438383
CC BY-SA 4.0
2020-08-06T09:12:20.403Z
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.
user2808642
CC BY-SA 4.0
2020-08-06T14:02:27.933Z
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?
user438383
<bioconductor><gwas><human-genome><phylogenetics><molecular-genetics>
Power calculation for GWAS/EWAS
# 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**: @gringer 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?  

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## 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  

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