/LR-Methyation

Analysis scripts for comparison between EPIC and Nanopore methylation data

Primary LanguageR

LR-Methyation

Analysis scripts for comparison between EPIC and Nanopore methylation data

Requirements

R

Required libraries:

  • ggplot2
  • optparse
  • dplyr
  • patchwork
  • ggpubr
  • ggseqlogo
  • stringr
  • tidyr
  • gridExtra
  • data.table

How to run

Analysis

Rscript ./scripts/main.R  \ 
        --nanopore $np_file \
        --epic $epic_file \
        --output $output_directory \
        --sample $sample_name

File requirments

$np_file modbam2bed output file with the following 13 fields (from https://github.com/epi2me-labs/modbam2bed): (highlighted fields are required, the other can be filled with any value)

  • 1 reference sequence name
  • 2 0-based start position
  • 3 0-based exclusive end position (invariably start + 1)
  • 4 Abbreviated name of modified-base examined
  • 5 "Score" 1000 * (Nmod + Ncanon) / (Nmod + Ncanon + Nno call + Nalt mod + Nfilt + Nsub + Ndel). The quantity reflects the extent to which the calculated modification frequency in Column 11 is confounded by the alternative calls. The denominator here is the total read coverage as given in Column 10.
  • 6 Strand (of reference sequence). Forward "+", or reverse "-".
  • 7-9 Ignore, included simply for compatibility.
  • 10 Read coverage at reference position including all canonical, modified, undecided (no calls and filtered), substitutions from reference, and deletions. Nmod + Ncanon + Nno call + Nalt mod + Nfilt + Nsub + Ndel
  • 11 Percentage of modified bases, as a proportion of canonical and modified (excluding no calls, filtered, substitutions, and deletions). 100 * Nmod / (Nmod + Nalt mod + Ncanon)
  • 12 Ncanon
  • 13 Nmod

$epic_file output of methylation calling with 2 columns containing:

  • probes id
  • beta value