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Pilot Projects
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find and download HapMap2 genotype data for CEU, YRI, and ASN (CHB and JPT) populations in plink format (use the one with all populations combined)
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use GCTA to calculate eigenvectors y eigenvalues of the hapmap genotype data
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plot the first few eigenvectors against each other
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download intrinsic growth data and run GWAS using plink (Table S1 from http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002525 - you may need to add a family id column to this file when running plink)
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re-run GWAS using the first 2 eigenvectors of genotype data as covariates
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write a short report describing what you have done
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Present results
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find and download HapMap2 genotype data for CEU, YRI, and ASN (CHB and JPT) populations in plink format (use the one with all populations combined)
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use GCTA to calculate eigenvectors y eigenvalues of the hapmap genotype data
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plot the first few eigenvectors against each other
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create a “phenotype” that is 1 if the individual belongs to CEU and for the other populations
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run GWAS using plink for this phenotype
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run GWAS again using the first 2 eigenvectors obtained with GCTA
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write a short report
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present