Step 2b: Optional QC for cis-eQTL Results

Overview

Step 2b is optional, it involves user-specified quality control based on dispersion parameter from step 1 results and genomic inflation factor from step2 results.

Getting Started

Example Scripts Location

The wrapper scripts and example data are located in the ./extdata folder: https://github.com/weizhou0/SAIGEQTL/tree/main/extdata

Check Installation instruction if you haven’t had SAIGE-QTL installed yet: Install SAIGE-QTL

Running step 2b

Pixi Installation

# Navigate to SAIGEQTL directory first
cd SAIGEQTL/extdata

pixi run --manifest-path=../pixi.toml Rscript step2b_QC_qtl.R  \
  --SAIGEstep1OutputPrefix=./output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1 \
  --SAIGEstep2OutputPrefix=./output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis \
  --gene=example_gene \
  --outPrefix=example_gene_output \
  --isPostStep2QC=FALSE \
  --phiUpper 1.5 \
  --lambdaLower 0.1 \
  --lambdaUpper 1.5

Input Files

1. step 1 and step 2 results (Required)

Since the optional quality control is based on parameters calculated from step 1 and 2, the output from both steps would be required to calculate corresponding parameters.

Key Parameters Explained

Parameter	Description	Example Value
--SAIGEstep1OutputPrefix	Path to step1 output filename (no suffix)	./output/nindep_100_ncell _100_lambda_2_tauIntraSample_0.5_gene_1
--SAIGEstep2OutputPrefix	Path to step2 output filename (no suffix)	./output/nindep_100_ncell _100_lambda_2_tauIntraSample_0.5_gene_1_cis
--gene	Gene name (for reporting only)	example_gene
--outPrefix	Output prefix for QC summary	example_gene_output
--sampleIDColinphenoFile	Sample ID column name	IND_ID
--isPostStep2QC	Whether to remove step1 and step2 outputs if they fail QC standards (logical)	FALSE
--outputPrefix	Prefix for output files	./output/analysis_gene1
--phiUpper	Upper bound for phi dispersion parameter	User-specified
--lambdaLower	Lower bound for GC lambda	User-specified
--lambdaUpper	Upper bound for GC lambda	User-specified

Output Files

Evaluation metric summary file

Contains dispersion and GC lambda estimation for this specific gene for record.