Quick Start

Table of contents

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

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.

Run metilene3

  • Unsupervised mode: with unsupervised mode, each sample will be regarded as one group.
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.

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).
    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].
  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.)