<commit_before>---
title: Introduction to eQTL analysis
author: <NAME>
---

# What are eQTL?

# Detecting eQTL

## Linear additive model

## Dominant/recessive model <commit_msg>Additional content.<commit_after>---
title: Introduction to eQTL analysis
author: <NAME>
---

# What are eQTL?


# Detecting eQTL
## How do we know whether a locus is associated with the expression of a gene?

<div class="multicolumn">
<div>
![](figure/genomic_locus.png)

</div>
<div>
* **Any given locus contains multiple SNPs.**
* Can determine genotypes for these SNPs in a (large) number of individuals.
* Measure gene expression for genes of interest.
* For each SNP/gene pair, assess the evidence that expression varies with genotype.
</div> 
</div>

## How do we know whether a locus is associated with the expression of a gene?

<div class="multicolumn">
<div>

 sample	   snp_1   snp_2   snp_3   ...
--------   -----   -----   -----  -----
sample 1    AA      AA      AB     ...
sample 2    AB      AB      AA     ...
sample 3    AB      BB      AB     ...
...        ...     ...      ...    ...

</div>
<div>
* Any given locus contains multiple SNPs.
* **Can determine genotypes for these SNPs in a (large) number of individuals.**
* Measure gene expression for genes of interest.
* For each SNP/gene pair, assess the evidence that expression varies with genotype.
</div> 
</div>

## How do we know whether a locus is associated with the expression of a gene?

<div class="multicolumn">
<div>

 sample	   gene_1   gene_2   gene_3   ...
--------   ------  ------    ------  -----
sample 1    7.3     12.8      6.5     ...
sample 2    10.9    9.6       8.8     ...
sample 3    9.5     10.7      15.1    ...
...         ...     ...       ...     ...

</div>
<div>
* Any given locus contains multiple SNPs.
* Can determine genotypes for these SNPs in a (large) number of individuals.
* **Measure gene expression for genes of interest.**
* For each SNP/gene pair, assess the evidence that expression varies with genotype.
</div> 
</div>

## How do we know whether a locus is associated with the expression of a gene?

<div class="multicolumn">
<div>
![](figure/snp_expression.png)
</div>
<div>
* Any given locus contains multiple SNPs.
* Can determine genotypes for these SNPs in a (large) number of individuals.
* Measure gene expression for genes of interest.
* **For each SNP/gene pair, assess the evidence that expression varies with genotype.**
</div> 
</div>


## Linear additive model

{'fraction_non_alphanumeric': 0.1308562197092084, 'fraction_numerical': 0.013731825525040387, 'mean_word_length': 2.351826792963464, 'pattern_counts': {'":': 0, '<': 29, '<?xml version=': 0, '>': 29, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '203072', 'n_tokens_mistral': 771, 'n_tokens_neox': 715, 'n_words': 311}