dmr_exportData

Plot figure or export data for DMRs/MRs in specific regions, such as DMRs overlapping mutation blocks or enhancer regions, etc.

Required Arguments

  • in_MRfolder or --input_mr_data_folder: Input MR data folder, which is the output file folder of dmr_analysis_block.

  • out_folder or --output_file_folder: Output file folder for exported MR/DMR data.

  • in_format or --input_file_format: Input file format: 0 for a BED format file where DMR/MR IDs are listed in the fourth column (e.g., chr18:mr0:mix:U), 1 for an exported file with 8 columns generated by dds_analysis “check_block_gene_inTAD” where all DMRs and mutation blocks are assigned to a putative target gene, and DMR/MR IDs are under the column “new_mr_sites”.

  • in_file or --input_file: A file containing DMR/MR IDs that will be used to extract the raw and smoothed methylation levels of DMRs/MRs listed in either a BED format file or an exported file from “dds_analysis check_block_gene_inTAD”.

Optional Arguments

  • processes or --number_of_processes: Number of parallel processes to be used for data extraction. Default is 5.

  • columnNumber or --input_file_bed_column: If the input file is a BED format file, this parameter specifies the column number of DMR/MR IDs. The default is 3, which represents the fourth column (since the index starts from 0).

  • columnName or --input_file_dds_column_name: If the input file is generated by “dds_analysis check_block_gene_inTAD”, this parameter specifies the column name of DMR/MR IDs. The default is “new_mr_sites”.

  • wtStr or --wildType_fileString: The file name pattern of the wild type/control sample files. For example, if a wild type/control file name starts with “gcb_meht1_*”, the value of this parameter should be “gcb” (which is the default setting in the program).

  • dotOrUnderscore or --column_splitBy_dotOrUnderscore: Use 0 for splitting column labels by dot (.), or 1 for splitting by underscore (_) in the file specified by in_data_file. Default is 0 (dot split column labels).