Mediated heritability estimation#

Schematic overview of SBayesC(R)O-AIAO Bayesian model integrating GWAS and molecular phenotype data

Summary-level AIAO model#

Options#

--sbayes CO#

Bayesian model used for parameter estimation.

--mcmc-type eieo#

Algorithm used for parameter estimation.

--ldm-eigen#

GWAS LD low-rank matrix, see GCTB for detail.

--ldm-eigen-gene#

xQTL LD low-rank matrix.

--beqtl-summary eqtlSummaryFile#

A common used format for molecular summary statistics, see .besd for details.

--add-gene-n gsamFile#

Store the sample sizes for each gene or each gene-SNP pair, see .gsam for details.

--beqtl-summary-gz eqtlSummaryGZFile#

Another more easy-used format for molecular summary statistics, see .query.gz for details.

--gwas-summary gwasFile#

COJO format GWAS summary statistics

Command#

BayesOmics64  --sbayes CO \
  --mcmc-type eieo \
  --ldm-eigen  ldmEigenFolder  \
  --ldm-eigen-gene  ldmEigenGeneFile  \
  --beqtl-summary-gz eqtlSummaryGZFile \ # or use --beqtl-summary eqtlSummaryFile
  --gwas-summary  gwasFile   \
  --out outFile

Examples#

### downlaod dataset
git clone git@github.com:ShouyeLiu/BayesOmics.git
## find data in the Cau folder: BayesOmics/samples/pseudo/data/Cau/summary/
sumPath="" # cauFolder path
summaryFile="pseudo-1kg-chr22-cau-h2snp0.4-h2med-0.4-h2cis-0.6-model"
outFile="res-"${summaryFile} ## outFilePath
### downlaod binary tool
cd MainPath ## your main Path
wget https://github.com/ShouyeLiu/BayesOmics/releases/latest/download/BayesOmics64-static
chmod 751 BayesOmics64-static

 BayesOmics64-static  --sbayes CO \
   --ldm-eigen ${sumPath}/${summaryFile} \
   --gwas-summary ${sumPath}/${summaryFile}.ma \
   --ldm-eigen-gene ${sumPath}/${summaryFile} \
   --beqtl-summary  ${sumPath}/${summaryFile} \
   --hsq 0.1  \
   --hsq-cis 0.1  \
   --mcmc-type aiao  \
   --chain-length 5000 \
   --burn-in 1800 \
   --seed 10  \
   --out-freq 500 \
   --out  outFile