Example Data and Projects

The following datasets are based off the 270 HapMap samples with simulated phenotype and clinical information for each sample. Genotypes and normalized log2 ratios were generated from Affymetrix's 500K Human Mapping Array. It is useful for demonstrating a variety of whole genome association workflows including data manipulation, quality assurance, association testing, and visualization of results.

HapMap 270 Affymetrix 500K

File Size File Type Description
HM_Sim_Pheno.zip 11KB Data Simulated phenotype and clinical data.
HM_500K_Geno.zip 21MB Data Actual genotypes for all 270 HapMap samples from the Affymetrix 500K array.
Simulated_HapMap_GWAS.zip 98MB Project This project contains all the datasets and results from the SNP Whole Genome Association Analysis tutorial.
HM_Sample_CNV_Data.zip 500MB Data This zip file contains:
  • Normalized log2 ratio for all 270 HapMap samples from the Affymetrix 500K array.
  • Simulated phenotype and clinical data.
  • NSP and STY matching spreadsheet.
HM_CNAM_22_Results.zip 283KB Data Results from running CNAM optimal segmenting on PCA corrected log ratios from chromosome 22 of HapMap samples on Affymetrix 500K array.
ROH_Tutorial.zip 245MB Project This project contains HapMap genotypes and B-allele frequencies used for the Runs of Homozygosity Tutorial.



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