Package index

Database Creation

Build and manage methylation databases from .ch3 files

make_mod_archive()

Create a Compressed Methylation Call Archive (.ch3) from a calls file.

make_mod_db()

Create a Modifications DuckDB from Parquet CH3 files (with optional sample naming)

Summarize Data

Summarize methylation data at different resolutions

summarize_mod_positions()

Summarize per-position methylation calls into a DuckDB table

summarize_mod_regions()

Summarize methylation by annotated regions

summarize_mod_windows()

Summarize methylation in sliding windows

summarize_mod_reads()

Summarize Reads in a Database

Differential Methylation

Detect and collapse differentially methylated regions

calc_mod_diff()

Calculate Differential Methylation

collapse_mod_windows()

Collapse Windows Based on Methylation Differences

Quality Control & Visualization

QC reports and plotting functions

run_mod_qc()

Quality Control Wrapper for Methylation Data

plot_mod_cov()

Calculate and Plot Coverage Statistics

plot_mod_diff()

Plot Differential Methylation Volcano Raster

plot_mod_diff_density()

Plot Case vs Control Methylation Fractions with Density-Weighted Points

plot_mod_modfrac()

Get Methylation Statistics from the Modifications Database

plot_mod_pca()

Perform PCA on Methylation Data

calc_mod_samplecor()

Correlation Matrix of Modified Sequence Data

Database Utilities

Inspect, query, and manage your database

get_mod_dbinfo()

Get Database Statistics

get_mod_tableinfo()

Get Table Information from mod Database

get_mod_cols()

Get Column Names from a DuckDB Table

get_mod_cpg_count()

Count unique CpG sites in a mod database table

get_mod_stats()

Compute Statistics for a Ch3 File

get_mod_table()

Collect Table from DuckDB Database as Tibble

export_mod_table()

Export Tables from the mod Database

remove_mod_table()

Remove a table from a database connection.

rename_mod_samples()

Rename sample names in a table

Read-Level Tools

Classify and filter individual reads

classify_mod_reads()

Classify Reads as Case or Control Based on Methylation Profiles

trim_mod_reads()

Trim methylation calls at the read ends in a mod database

filter_mod_table()

Filter a DuckDB Table and Save to a New Table

Advanced Queries

Run custom SQL or dplyr queries on your database

run_mod_sql()

Execute a query on a mod Database

run_mod_dplyr()

Execute an Expression on a DuckDB Table with Optional Materialization

Pipeline

Run a full analysis in one command

run_mod_analysis()

Run Differential Analysis on Methylation Data

Package

Package-level documentation and internal classes

ModSeqR-package ModSeqR

ModSeqR: Methylation Data Analysis from Nanopore Sequencing

print(<mod_db>)

Helper Function to Print Database Tables