Question: GWAS & Logistic regression in R
0
gravatar for carlos.maldonadomota
2.2 years ago by
carlos.maldonadomota0 wrote:

Hi

I have my genotype data and my phenotype data, I made GWAS with GAPIT tool, but now I would like to use the logistic regression analysis in R, which software is the appropriate ? What would be the first step to work with the data?

Thanks.

R • 1.4k views
ADD COMMENTlink modified 2.2 years ago by Jeremy Leipzig18k • written 2.2 years ago by carlos.maldonadomota0
1
gravatar for Jeremy Leipzig
2.2 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

A logistic regression is where your dependent, outcome variable is dichotomous or binary (aka logical).

GAPIT is a mixed model linear regression, which means it tries to divide the regressors into fixed and random effects. This is super important in agriculture where most of all the GWAS signals end up being SNPs associated with some inbred line.

They correct for this by this assigning fixed effects to SNPs and call the population a random effect, or vice-versa.

GAPIT assumes a continuous linear outcome variable. There is such a thing as mixed model logistic regression. Actually, I wouldn't be surprised if GAPIT has a logistic method hiding somewhere.

So...is your outcome a number or a category?

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Jeremy Leipzig18k

It is a number (0,1)

ADD REPLYlink written 2.2 years ago by carlos.maldonadomota0

Is it continuous?

ADD REPLYlink written 2.2 years ago by Jeremy Leipzig18k

No,I just have 0 and 1

ADD REPLYlink written 2.2 years ago by carlos.maldonadomota0
1

It's probably still ok to use GAPIT for this, you just have to round the responses to 0 or 1, assuming these responses are ordered in some meaningful way

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Jeremy Leipzig18k
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