Tutorials

Prepare datasets

### downlaod dataset
curPath="$PWD"
git clone https://github.com/ShouyeLiu/BayesOmics.git
### downlaod binary tool
wget https://github.com/ShouyeLiu/BayesOmics/releases/latest/download/BayesOmics64-static
chmod 751 ${curPath}/BayesOmics64-static

Extract simulated dataset

BayesOmics64="${curPath}/BayesOmics64-static"
## find data in the Cau folder: BayesOmics/samples/pseudo/data/Cau/summary/
datPath="${curPath}/BayesOmics/samples/pseudo/data/Cau/"
indDatPath=${datPath}/ind/
sumPath=${datPath}/summary/
filename="pseudo-1kg-chr22-cau-h2snp0.4-h2med-0.4-h2cis-0.6-model"
outPath="${curPath}/out/"
mkdir -p ${outPath}

trainBfile="${indDatPath}/${filename}"
snplist="${indDatPath}/${filename}.ma.snplist"
indlist="${indDatPath}/${filename}.indlist"
phenoFile="${indDatPath}/${filename}.pheno"
plistFile="${indDatPath}/${filename}.plist"
indGenelistFile=${indlist}

blockInfo="${curPath}/BayesOmics/samples/pseudo/data/genotype/param-ref4cM_v37.pos"

flistFile="${sumPath}/${filename}.flist"
gwasMaFile=${sumPath}/${filename}.ma
xqtlFile=${outPath}/${filename}

gwasLDfolder="${outPath}/${filename}"
xqtlLDFile=${outPath}/${filename}
outSBCOFile="${outPath}/${filename}.sbco"
outBCOFile="${outPath}/${filename}.bco"
mkdir -p ${gwasLDfolder}

Step 1. Generate low-rank GWAS LD reference

${BayesOmics64} \
   --bfile ${trainBfile}  \
   --extract  ${snplist} \
   --keep  ${indlistFile} \
   --make-block-ldm  \
   --block-info ${blockInfo} \
   --out ${gwasLDfolder}

${BayesOmics64} \
   --ldm ${gwasLDfolder} \
   --merge-block-ldm-info  \
   --out ${gwasLDfolder}

${BayesOmics64} \
   --ldm ${gwasLDfolder} \
   --make-ldm-eigen  \
   --out ${gwasLDfolder}
 ## end

Step 2. Generate low-rank xQTL LD reference

Convert xQTL summary statistic to smr BESD format. Before do this using sample dataset, we need to change filePath in flistFile. See GCTA SMR for details

## Assume sample data is here
mainPath="${datPath}"
oldPath="/Users/uqsliu28/Documents/personal/SbayesAnno/samples//summary/"
newUpdatedPath="${sumPath}" ## the location of gene phenotype

## Before changing path
head ${flistFile}

## then replace genePhenotypePath in the plist file by using command
sed -i -e "s|${oldPath}|${newUpdatedPath}|" ${flistFile}

## After changing path
head ${flistFile}

Now convert flist file into BESD format

${BayesOmics64} \
  --eqtl-flist ${flistFile}  \
  --make-besd \
  --out ${xqtlFile}

Generate xQTL low-rank LD matrix based on BESD format

${BayesOmics64} \
  --bfile ${trainBfile}  \
  --beqtl-summary ${xqtlFile} \
  --extract ${snplist} \
  --keep  ${indlist} \
  --make-eigen-gene \
  --out ${xqtlLDFile}

Save xQTL summary statistic to gz format

${BayesOmics64} \
  --beqtl-summary ${xqtlFile}  \
  --make-query \
  --out ${xqtlFile}.q

Step 3. Perform (S)BayesOmics analysis

Summary-level analysis

${BayesOmics64} \
  --sbayes CO \
  --ldm-eigen  ${gwasLDfolder}  \
  --ldm-eigen-gene  ${xqtlLDFile}  \
  --ldm-eigen-cutoff 0.995  \
  --ldm-eigen-gene-cutoff 0.995  \
  --beqtl-summary ${xqtlFile}  \
  --gwas-summary  ${gwasMaFile}  \
  --piEffEqtl 0.01 \
  --piEffNonEqtl 0.01 \
  --hsq  0.1\
  --hsq-cis 0.1 \
  --sampleVare   \
  --sampleVarEps  \
  --chain-length 1000  \
  --burn-in 400  \
  --out-freq 100   \
  --out ${outSBCOFile}