dmr_selected4plot

Plot figures or export methylation data for selected DMR/MRs.

Required

  • -inDMR IN_DMR_FILE: A file generated after performing ‘dmr_analysis_block’ and ‘dmr_combine_multChrs4rank,’ which contains DMR information and logReg probability values for each MR, in addition to the main feature scores exported from dmr_analysis_block. This file is usually exported for each chromosome under the ‘plots’ folder in the output folder of dmr_analysis_block.

  • -inData IN_DATA_FILE: A file containing raw DNA methylation data of all MRs in a chromosome, exported after running ‘dmr_analysis_block.’ This file is stored in each chromosome’s output folder. For example, a file named ‘chrY_MR_data4maxBlockDistance_250_minBlockSize_5_data.txt.gz’ is stored in the ‘chrY’ output folder after running ‘dmr_analysis_block.’

  • -inFolder IN_DATA_FOLDER: Path of a file folder that contains all the files mentioned in -inDMR and -inData. For example, ‘out/chrY’ is the path that stores DMR/MR raw data for the ‘chrY’ chromosome after running dmr_analysis_block and dmr_combine_multChrs4rank.

Optional Parameters

  • -inDMRFolder: A subfolder for storing exported MR/DMRs in each chromosome after running dmr_analysis_block. The default is ‘plots/’ under --in_data_folder.

  • -inAcCut: A range of clustering accuracy to consider in the program. The default is ‘0.0,1.0,’ which means between 0.0 and 1.0.

  • -inDmrSt: A string used in --inDMR_file that represents the predicted DMR. The default is ‘D,’ representing predicted DMR.

  • -inOtCod IN_OTHER_CONDITION: A string type for selecting DMR from the whole data, such as logReg_proba, min_dmr,max_dmr, top_to_down, top_rank, down_rank, or None. The default is down_rank_10 (10%).

  • -inDstart: The position of the data start column in a file inputted from --in_data_file. The default is 3 because the first three columns are chromosome positions (chrom, start_post, end_post), followed by data columns (data1, data2, …).

  • -inIsExt: Whether to export data (1) or not (0) for selected DMR/MRs. The default is 0, indicating not exporting data.

  • -dotOrUnderscore: Use 0 for dot (‘.’) split column labels or 1 for underscore (‘_’) split column labels in the file specified by --in_data_file. The default is 0 (dot split column labels).

  • -inIsPlt or --is_plot: Whether to plot the figure (1) or not (0) for selected DMR/MRs. The default is 0, indicating not plotting the figure.

  • -inIsPas or --is_pause: Whether to pause (1) or continue (0) in the loop. The default is 0, indicating continuing in the loop for all input DMR/MRs.

  • -inLogNm or --in_Logger_number: Logger number for recording screen displays. The default is 0.

  • -inOutFd or --out_folder: Path for the output file folder. The default is ‘out/’.

  • -inNdChk or --needs_check_mr: String ID of selected DMR/MRs that will be checked/plotted/data exported, comma-separated. For example, ‘mr10,mr111.’ The default is not to check.

  • -dpi or --figure_dpi: Export figure resolution in DPI. The default dpi is 30.

  • -format or --figure_format: File format of the exported figure, such as jpg, svg, pdf, or png. The default is pdf.

  • -wtStr or --wildType_fileString: A file name of the wild-type condition file, which should start with specific characters. For example, if a file name starts with ‘gcb_meth1_*’ is a wild-type/control sample, then --wildType_fileString is ‘gcb,’ which is the default setting in the program.