reference

This folder containers publicly available reference, derived from different resources as documented below.

• hapgen folder contains artificially generated genotypes in plink format for N=10k individuals and M=149454 SNPs, with reasonably realistic LD structure representing chromosome 21 in EUR population (chr21 is choosen because it is the shortest chromosome in human genome); the data was generated using HapGen2 software.

• ldsc folder contains certain files copied from https://alkesgroup.broadinstitute.org/LDSCORE needed to run basic LD score regression analysis. Some of this data is derived, e.g. ldsc/1000G_EUR_Phase3_baseline_split/base is extracted from 1000G_Phase3_baseline_ldscores.tgz using just the base column (i.e. total LD score).

• ldsc/1000G_EUR_Phase3_plink contains reference data for the MiXeR tool. The reason for placing MiXeR data within ldsc is because it was derived from LDSC reference data (M=9997231 SNPs, N=489 individuals EUR ancestry).

• pleiofdr/9545380_ref folder contains reference data for pleioFDR analysis.

• pleiofdr/demo_data folder contains a demo dataset for pleioFDR analysis, constrained to a very few SNPs so that the analysis runs very fast. You can not use this reference for real analysis - it's only a playground to see if pleioFDR runs well on your machine. This data includes CTG_COG_2018_DEMO.mat and SSGAC_EDU_2016_DEMO.mat from these publications:

  • https://ctg.cncr.nl/software/summary_statistics , Summary statistics for intelligence, wave 2 from Jeanne Savage et al., 2018
  • https://www.thessgac.org/data , Lee et al. (2018). Gene discovery and polygenic prediction from a 1.1-million-person GWAS of educational attainment. Nature Genetics, 50(8), 1112-1121. doi: 10.1038/s41588-018-0147-3