dds_geneRanking

Select top-ranked genes and blocks from the final prediction.

Optional Arguments:

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

Required Arguments:

  • -inUqGene IN_UNIQUE_GENE_FILE, –in_unique_gene_file IN_UNIQUE_GENE_FILE: Input a file containing a list of unique genes exported from dds_analysis. This file should contain information about the unique genes identified in the analysis.

  • -inDEGFile IN_DEG_FILE, –in_DEG_file IN_DEG_FILE: Input file containing a list of differentially expressed genes exported from BayesPI-BAR2. This file should contain information about the differentially expressed genes.

  • -inDMRFile IN_DMR_FILE, –in_DMR_file IN_DMR_FILE: Input file containing differential methylation region information exported from dmr_analysis. This file should contain information about the differential methylation regions.

Optional Arguments with Default Values:

  • -inCutoff, –in_cutoff_pval4score: Cutoff probability value for selecting top-ranked genes. Default: 0.5.

  • -TSS, –TSS_score: Weight score for TSS (Transcription Start Site). Default: 4.0.

  • -gene, –gene_score: Weight score for gene. Default: 2.0.

  • -TES, –TES_score: Weight score for TES (Transcription End Site). Default: 2.0.

  • -dist, –dist_score: Weight score for 5 distance regions. Default: 1.0.

  • -enhancer, –enhancer_score: Weight score for enhancer. Default: 3.0.