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README.md
mini-gwas-data.zip
minigwas.R

README.md

title keywords difficulty author
miniGWAS
genetic association
GWAS
medium
Miguel Pereira

Description

You have a dataset with phenotype and genotype data and the goal is to discover newe genetic variants associated with the outcome 'fvcmax', a measure of lung function.

Objectives

  1. Run a genetic association analysis to identify which SNPs are associated with FVC (variable 'fvcmax' in the dataset).

Things to consider:

  1. The phenotype and genotype data are in different files. There is one file with phenotype and outcome and 22 files with the genotype data, one file per chromossome.

  2. The goal is to open one file at a time, run a regression analysis adjusting for the phenotype variables and one SNP in each regression.

  3. After you obtain the regression results for each SNP, select the ones that are signigicantly related with fvcmax. All regression analyses should be adjusted for age, sex and the principal components (PCs), which are measure of population ancestry. Note: you need to consider a p-value correction method to obtain a significance thresold (e.g. Bonferroni correction, the most commonly used method in genetic association analysis).