Quick Start

Table of contents

  1. Run metilene3
  2. Input file(s)
  3. Output files

Run metilene3

  • Unsupervised mode: with unsupervised mode, only the methylation matrix should be provided.
python /path_to_metilene3/metilene3.py -i methylation.tsv -o /output_dir

Or,

  • Supervised mode: with supervised mode, each sample should be assigned to a group, which should be recorded in the samples_groups.tsv.
python /path_to_metilene3/metilene3.py -i methylation.tsv -g samples_groups.tsv -o /output_dir

More parameters could be added. Please check unsupervised mode and supervised mode for details.

Input file(s)

  1. CpG methylation matrix: methylation.tsv
    This matrix should include chromosome, position and CpG methylation levels for each sample. Click to see an example!

  2. Group information table: samples_groups.tsv (optional, supervised mode only)
    If you already have the group information and wish to compare different groups, you can provide this file to metilene3 with this format.

Output files

  1. A HTML report summerizing DMRs and other results: /output_dir/report.html.

  2. A tab-separated table containing all DMRs found by metilene3: /output_dir/DMRs.tsv
    (and /output_dir/DMRs-unsupervised.tsv for DMRs found with unsupervised mode) together with the sample-level DMR methylation rates /output_dir/DMR-met.tsv.
    Click here to understand it!

  3. A tab-separated table containing name and order (ID) for each group: /output_dir/group-ID.tsv.

  4. A tab-separated table containing cluster ID for each sample: /output_dir/clusters.tsv.
    (unsupervised mode only)

  5. Figures under the folder /output_dir/:
    (only with unsupervised mode and the parameter visualization -plot is set to True)
    1. DMR tree: DMTree.[jpg, pdf], showing the hierarchical structure based on the sum of DMR weights (branch lengths) between two branches. You can also find the DMTree in Newick tree format: DMTree.nwk.
    2. PCA 2D-visualization and clustering heatmap based on sample-level DMR methylation ratios:
      [PCA, heatmap].[jpg, pdf]. The source data can be found in tsv files.
  6. GSEA results: /output_dir/GSEA/ (and /output_dir/GSEA-unsupervised/ for unsupervised DMRs).
    (only if the parameter annotation -anno and the parameter GSEA -gsea are set.)