Meth_Comp usage

Generate a fully responsive interactive HTML report for significant differentially methylated intervals found with pycoMeth Meth_Comp. At the moment only data binned by intervals with Interval_Aggregate are supported.

Example usage

• Python API usage
• Shell CLI usage

Input files

pycoMeth CpG_Aggregate or Interval_Aggregate output file

A TSV output files generated with pycoMeth Meth_comp with data binned by intervals using pycoMeth Interval_Aggregate.

Reference GFF3 file

An Ensembl GFF3 file containing genomic annotations to extract transcripts with TSS close to the top most significant CpG Intervals.

• Main Ensembl: https://www.ensembl.org/index.html
• Ensembl Bacteria: http://bacteria.ensembl.org/index.html
• Ensembl Fungi: http://fungi.ensembl.org/index.html
• Ensembl Plants: http://plants.ensembl.org/index.html
• Ensembl Protists: http://protists.ensembl.org/index.html
• Ensembl Metazoa: http://metazoa.ensembl.org/index.html

Reference FASTA file

FASTA reference file used for read alignment and Nanopolish. This file is required and used to sort the chromosomes in the ideogram plot.

Output files

Summary HTML report (pycoMeth_summary_report.html)

Entry point to the report containing information of methylation status at genomic level.

Example Summary report

The report contains the following items:

• Overall summary Simple table containing counts of intervals and CpGs significantly differentially methylated.

• Methylation category counts by sample Interactive plotly stacked bar plot showing the number of methylated, unmethylated and ambiguous intervals for each samples.

• Methylation log-likelihood ratio by CpG interval Interactive plotly heatmap of the median llr for all significant intervals. Sites are ordered by genomic coordinates and samples are clustered by hierarchical clustering.

• Distribution of CpG methylation log-likelihood ratio by sample Interactive plotly ridgeplot of median llr distribution for all sample at interval resolution. Samples are ordered by descending overall median llr.

• Ideogram of the distribution of significant CpG intervals by chromosomic intervals

Interactive chromosome ideogram plot showing the number of significant sites binned in large intervals.

• Top differentially methylated intervals Table containing details of the n top differentially methylated candidates ranked by adjusted pvalue. The table contains links to individual intervals HTML reports.

Top intervals HTML reports

Individual reports for the top differentially methylated interval candidates. The right side navigation bar allows to explore all the other intervals or go back to the summary report.

Example Interval report

The report contains the following items:

• Interval details Simple table containing details about the interval

• Methylation log-likelihood ratio by CpG position Interactive plotly heatmap of the median llr for all CpG positions in the interval. Sites are ordered by genomic coordinates and samples are clustered by hierarchical clustering.

• Distribution of CpG methylation log-likelihood ratio by sample Interactive plotly ridgeplot of median llr distribution for all sample at CpG resolution. Samples are ordered by descending overall median llr.

• Closest transcripts TSS Table containing the list of all transcripts having their TSS within 100kb of the interval edges. Transcripts are ranked by TSS distance to the interval