Genetic European Variation in Health and Disease - Data Analytics Assignment Help

Assignment Task

The experiment and data
The experiment: Among the recent large scale human genomics resources is Genetic European Variation in Health and Disease (gEUVADIS) - see the following links for relevant descriptions and information:
with a samples from 4 different European populations (5 populations total). Each of these individuals were part of the 1000 Genomes project and their genomes were sequenced and analyzed to identify SNP geno- types. For expression profiling, lympoblastoid cell lines (LCL) were generated from each sample and mRNA levels were quantified through RNA sequencing.

Each of these gene expression measurements may be thought of as a phenotype and one can do a GWAS analysis on each individually, which is called an ‘expression Quantitative Trait Locus’ or ‘eQTL’ analysis, an unnecessarily fancy name for a GWAS when the phenotype is gene expression!
What you have been provided is a small subset of these data that are publicly available. Specifically, you have been provided 50,000 of the SNP genotypes for 344 samples from the CEU (Utah residents with European ancestry), FIN (Finns), GBR (British) and, TSI (Toscani) population.

For these same individuals, you have also been provided the expression levels of five genes. You have also been provided information on the population and gender of each of these individuals, and information regarding the position of each gene and SNP in the genome.

The data: These have been provided to you in five total files: ‘phenotypes.csv’,‘genotypes.csv’, ‘covars.csv’, ‘gene info.csv’,‘SNP info.csv’. ‘phenotypes.csv’ contains the phenotype data for 344 samples and 5 genes. ‘genotypes.csv’ contains the SNP data for 344 samples and 50000 genotypes. ‘covars.csv’ contains the population origin and gender information for the 344 samples.

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