dmr_combine_multChrs4rank

This program is used to combine DMR/MRs from multiple chromosomes.

Required Parameters

  • inChrs or --in_chroms_number: A string of chromosomes that need to be combined, separated by commas. For example: chr1,chr2,chr3.

  • inFold or --in_file_folder: The file folder containing MR data for each chromosome that is exported by dmr_analysis_block.

Optional Parameters

  • inSFold or --in_File_subFolder: The subfolder of exported MR data in each chromosome based on dmr_analysis_block. Default is “plots” located under each chromosome folder.

  • inMPer or --in_minimum_percentage_changes: The minimum percentage of data points in an MR with a predefined methylation change greater than a cutoff. Default is 0.0001.

  • inPC or --in_Pvalue_cutoff: The P-value cutoff for the significance test. Default is 0.05.

  • inIsSmd or --in_is_smoothed_data: The type of data used for the results: raw = 0, interpolated = 1, or smoothed = 2. Default is 0.

  • inAC or --in_accuracy_cutoff_range: The range of clustering accuracy. Default includes all values from 0.0 to 1.0, specified as 0.0,1.1.

  • inDMRst or --in_DMR_string_type: A string used to represent predicted DMRs in the file. Default is “D” for predicted DMRs.

  • inLRpb or --in_LogReg_proba: A probability value used by logistic regression to select DMRs. Default is 0.8.

  • inMT or --in_moderate_ttest: The type of significance test to evaluate: 0 for standard T-test, 1 for moderate T-test, and 2 for KS-test. Default is 0.

  • inLMH or --in_low_median_high_cutoff: Use high, median, or low minimum percentage change for DMR ranking. Default is “high”.

  • inFEstr or --in_file_ending_string: The file name ending string used to search for result files in the result folder (e.g., chrY/plots/). Default is “_all”.