SuRE-raQTL-scripts

This repos contains scripts and data associated with the manuscript "J. van Arensbergen et al: Systematic identification of human SNPs affecting regulatory element activity."

These are scripts and small data files used to generate the lists of raQTLs. The scripts are used as follows:

1. downsampling_reformatting_normalizing_combining_SuRE-counts_LP190327.R extracts and reformats relevant data from the SuRE-counts data files, which are generated by the preprocessing pipeline (see github).
   This script uses the accompanying data files from this repos for downsampling some of the input data files.
2. size_reduction_SuRE-count_files_JvA190328.R reduces the size of the data files generated in the first step.
3. wilcox_analysis_and_dataframe_construction_JvA190328.R performs the actual statistical testing and filtering.