SAIGE-QTL Dynamic Step 3

Step 3 combines p-values using cauchy combination/ACAT test to obtain gene-level p-values.

Preprocessing for step 3

1. Run the following script 001_concatenate.sh to concatenate all genes’ P values from step 2.

2. Run the following script 002_split.sh to split the vectors into separated columns for each interaction term.

3. Run the following script 003_filter_maf.sh to filter to common variants.

Running step 3

For Step 3, no specific environment is required, so it can be run outside of the container. We provide the R script step3_0.2.5.1_cl.R and example commands in a shell script. After running Step 3, please run qvalue() in R on the main-effect P-values and on each interaction term, then filter by FDR to obtain the eGenes.

Example script: step3_0.2.5.1.sh

Rscript step3_0.2.5.1_cl.R \
  --input "/.../filtered_maf_split_file.txt" \
  --outdir "/.../step3_output/"