dmr_cal2chromSegment_percent

Calculate percentage of DMRs in chromatin segment (e.g., generated from ENCODE predictions of 6 human cell lines)

Required:

  • -inOFolder IN_OUTFILE_FOLDER, --in_outFile_folder IN_OUTFILE_FOLDER: Input file folder for chromatin segment out file, for example, export files from “dmr_map2chromSegment”.

  • -inOFile IN_OUTFILE_NAME, --in_outFile_name IN_OUTFILE_NAME: Output file name of percentage DMR that will be calculated in chromatin segment regions.

  • -inFileStr IN_FILENAME_STRING, --in_fileName_string IN_FILENAME_STRING: Input file name string that will be searched (e.g., 24_chroms_high_miniPercentChange_gt_0.0001_Pcutoff_0.05_isSmooth_2_isModTest_0__all_dmrRanking_top_0.95_minLogReg_proba_0.7*) under folder –in_outFile_folder.

Optional, has default values:

  • -inLRpb , --in_LogReg_proba: A probability value used by logistic Regression to select DMRs. The default is 0.8.