eQTL-mapping

Software to map eQTLs, (cis- and trans-eQTLs), as well as sQTLs by comparing gene expression data with genotype data with R's Matrix eQTL package. This software, as a whole, can:

• map basic eQTLs
• map cis- and trans-eQTLs
• map sQTLs
• prepare data sets for Matrix eQTL input
• calculate MAF

This software is still under development

Set-up

Your gene expression data file and your genotype data file should be prepared for input into the Matrix eQTL package. By doing so, the data created will be saved in /data_preparation/RData/.

How do we prepare data?

Note: The MAF is calculated automatically at this step.

• Open a terminal in the R project (root folder).
• Run the following command: Rscript --vanilla ./data_preparation/prepare_data.R “your_genotype_data“ “your_gene_expression_data”
• The resulting *.RData file will appear in the /RData/ folder.
• Next your SNP and Gene position files should be set-up. They have to have the exact format described here for SNP positions and here for Gene positions.

Mapping basic eQTLs

• Run: Rscript --vanilla ./analysis/basic_eQTL.R
• The results are now in your /Users/your_name/Documents/R-Output/basic folder.

Mapping cis- and trans-eQTLs

• Run: Rscript --vanilla ./analysis/cis-trans-eQTL.R “your_gene_positions” “your_snp_positions” “location_to_RData_file” “cis_treshold_e.g._1e-5” “trans_treshold_e.g.1e-5” “cisDist_e.g._1e6”
• The results are now in your /Users/your_name/Documents/R-Output/cis & /Users/your_name/Documents/R-Output/trans folder.

Data file conversion (Specific for personal use only)

A runnable jar converts Gene positions and SNP position files to the desired format.

To run: java -jar ConvertPositionFile.jar "/Users/your_username/path/to/file.txt" "/Users/your_username/path/to/your_output_file_name.txt” “file_type”

• Note that you must have java installed on your system.
• You should use full paths to the files, else you will receive an error.
• The file type can either be gene or snp, depending on what sort of file you want to change.