# How to pass through phenotypes in model after regression analysis?

**URL:** https://discuss.hail.is/t/how-to-pass-through-phenotypes-in-model-after-regression-analysis/2259
**Category:** Hail Query & hailctl
**Created:** [September 22, 2021, 5:28am UTC](https://discuss.hail.is/t/how-to-pass-through-phenotypes-in-model-after-regression-analysis/2259 "2021-09-22T05:28:43Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![Abhishek](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/abhishek/32/570_2.png) [@Abhishek](https://discuss.hail.is/u/Abhishek)
#### Post date: [September 22, 2021, 5:28am UTC](https://discuss.hail.is/t/how-to-pass-through-phenotypes-in-model-after-regression-analysis/2259/1 "2021-09-22T05:28:43Z")

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I am currently performing regression analysis on a large dataset. I had my data annotated with phenotypes.

However, after performing regression, the phenotypes aren’t preserved in the model. It helps in analysing which phenotype is not falling on the regression curve.

The only way to do is to annotate phenotypes again after regression.

```auto
gwas_log = hl.logistic_regression_rows(test=test, y=y, x=x, covariates=covariates, pass_through=pass_through)
gwas_log = gwas_log.annotate(pheno=pheno_keys)

```

There is a `pass_through` method but it only works for variants. Is there any method for samples or phenotypes?

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### Author: ![kumarveerapen](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/kumarveerapen/32/355_2.png) [@kumarveerapen](https://discuss.hail.is/u/kumarveerapen)
#### Post date: [September 22, 2021, 1:14pm UTC](https://discuss.hail.is/t/how-to-pass-through-phenotypes-in-model-after-regression-analysis/2259/2 "2021-09-22T13:14:50Z")

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Hi, @Abhishek ! Thanks for your question. As far as I have run my analysis, I have merged/annotated the phenotypes again post regression. But perhaps, @johnc1231 may have a clearer answer to this which I have not observed and could learn from 🙂

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### Author: ![johnc1231](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/johnc1231/32/286_2.png) [@johnc1231](https://discuss.hail.is/u/johnc1231)
#### Post date: [September 22, 2021, 1:26pm UTC](https://discuss.hail.is/t/how-to-pass-through-phenotypes-in-model-after-regression-analysis/2259/3 "2021-09-22T13:26:29Z")

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What is `pheno_keys` in this case? I don’t really understand what you’re trying to do.

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<div class="post-metadata">

### Author: ![Abhishek](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/abhishek/32/570_2.png) [@Abhishek](https://discuss.hail.is/u/Abhishek)
#### Post date: [September 23, 2021, 6:03am UTC](https://discuss.hail.is/t/how-to-pass-through-phenotypes-in-model-after-regression-analysis/2259/4 "2021-09-23T06:03:08Z")

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It was a sample code for reference but I will the keys here as requested:

- test=`firth`

- x=`mt.add2` where `add2` is the additive model for gene(burden) matrix

- y=`mt.pheno.values()` which results in a list of phenotypes `[SuperPopulation, Population, CoffeeAddiction]`

- covariates=`[1.0]`

In summary, I am trying to perform All by All GWAS(therefore a list of phenotypes).