combine_dmr_deg2block

Combine information from DMR, DEG, and mutation blocks.

Optional Arguments:

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

Required Arguments:

  • -in_SBfile IN_SORTEDBLOCK_PATIENT_FILE, –in_sortedBlock_patient_file IN_SORTEDBLOCK_PATIENT_FILE: Bpb3 exported mutation block summary position file in BED format and sorted by chromosome and position, where patient IDs are added by dds_analysis find_block_patientID.

  • -in_DMRfile IN_DMR_FILE, –in_dmr_file IN_DMR_FILE: bpb3 block summary file with DMR information that is exported by dds_analysis map_block2dmr.

  • -in_DEGfiles IN_DEG_FOLDER_AND_FILE_SUFFIX, –in_deg_folder_and_file_suffix: Path of a file folder that contains results exported by dds_analysis find_geneExp4block, where DEG information is added to blocks (e.g., file_path/*.tsv).

Optional Arguments with Default Values:

  • -outFold, –out_file_folder: Path of output file folder.