find_enhancer_target_genes

Find enhancers and their target genes that overlap with mutation blocks associated with a selected gene.

Optional Arguments:

  • -h, –help: Show the help message and exit.

Required Arguments:

  • -inEnhancerF IN_ENHANCER_FILE_FOLDER, –in_enhancer_file_folder IN_ENHANCER_FILE_FOLDER: File folder containing enhancer files. Assumes all files end with *.bed. This folder should contain the enhancer files used for analysis.

  • -inDDSFile IN_DDS_FILE, –in_DDS_file IN_DDS_FILE: File name of the DDS (Disease-Enhancer-Target gene) final exported ranked gene list. This file contains the ranked gene list generated by the DDS analysis.

  • -inGene IN_SELECTED_GENE, –in_selected_gene IN_SELECTED_GENE: Gene name in the DDS export file to be searched for overlapping with enhancers. Specify the gene name for which you want to find enhancer-target gene associations.

  • -outFolder OUT_FOLDER, –out_folder OUT_FOLDER: Output file folder name. Specify the folder where the output files will be saved.

Optional Arguments with Default Values:

  • -isAll, –is_all_blocks: Whether to use all blocks or only enhancer-associated blocks for the enhancer-gene search. Default: enhancer-only blocks. If this option is used, only the blocks associated with enhancers will be considered for the enhancer-gene search.