Question: Basic Conception On Gwas
1
gravatar for Lds
7.3 years ago by
Lds390
Lds390 wrote:

Hi all,

I'm a new on Genome-wide association study. I just want to know some simple ideas on GWAS as follows,

  1. What's the statistical power in GWAS, how to calculate it?

  2. Some studies may contain multi-stage GWA-studies, why should they do this?

  3. For the Manhattan plot, the values for Y-axis may be Fst or -log(P), I know how to calculate the Fst, but for -log(P), what P stands for? How to calculate it, I mean the math approach.

  4. There may be a regression model for the outcome, such as linear regression for a quantitative trait or logistic regression for a qualitative trait, what the model looks like?

Maybe some can show some reference here to guide me to understand such questions filled in my head. Thanks in advance.

Linus

p-value gwas • 3.3k views
ADD COMMENTlink written 7.3 years ago by Lds390
1

I would suggest taking a look at this lecture:

http://www.stats.ox.ac.uk/~mcvean/gwa4.pdf

it is very informative.

ADD REPLYlink written 7.3 years ago by Zev.Kronenberg11k

I would suggest starting with a good review article.

http://www.nature.com/nrg/journal/v6/n2/abs/nrg1521.html

Genome-wide association studies for common diseases and complex traits

ADD REPLYlink written 7.3 years ago by Zev.Kronenberg11k
1
gravatar for Darren J. Fitzpatrick
7.2 years ago by
Ireland/ United Kingdom
Darren J. Fitzpatrick1.1k wrote:

STATISTICAL GENETICS: Gene Mapping Through Linkage and Association is an excellent introduction.

It has chapters addressing your specific questions!

ADD COMMENTlink written 7.2 years ago by Darren J. Fitzpatrick1.1k
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