Example data used in tutorial of HEIG (v1.2.0)

The repository contains example data used in tutorial of HEIG v1.2.0. Note, this data is not compatible with v1.0.0, and some options are supported in v1.1.0. HEIG is a statistical framework for efficiently conducting joint analysis for large-scale imaging and genetic data.

The dataset has the following file structures:

• input
  • images1: 500 simulated images
  • images2: 500 simulated images
  • genotype: genotype data in PLINK bfile
  • misc: miscellaneous files
  • ldr_sumstats: 19 LDR GWAS summary statistic files of the superior fronto-occipital fasciculus
  • ld_regu8580: LD matrices with regularization {85%,80%}, including ~460,000 genotype array SNPs
  • ld_regu7570: LD matrices with regularization {75%,70%}, including ~460,000 genotype array SNPs
  • visualization: example files for visualization
• output
  • fpca: results of functional PCA
  • genotype: hail.MatrixTable of genotype data
  • gwas: LDR GWAS results generated by HEIG
  • herigc: results of heritability and (cross-trait) genetic correlation analysis
  • images: preprocessed 1000 images in H5DF file
  • ldr: LDRs constructed from 1000 images
  • sumstats: preprocessed 19 LDR GWAS summary statistic files of the superior fronto-occipital fasciculus
  • visualization: visualization results
  • voxelgwas: voxel-level GWAS results

The results in ouput are produced by data in input, which can verify if the user runs the code correctly.