Package index • ModSeqR

All functions

ModSeqR-package ModSeqR: ModSeqR: Methylation Data Analysis from Nanopore Sequencing
calc_mod_diff(): Calculate Differential Methylation
calc_mod_samplecor(): Correlation Matrix of Modified Sequence Data
classify_mod_reads(): Classify Reads as Case or Control Based on Methylation Profiles
collapse_mod_windows(): Collapse Windows Based on Methylation Differences
export_mod_table(): Export Tables from the mod Database
filter_mod_table(): Filter a DuckDB Table and Save to a New Table
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_dbinfo(): Get Database Statistics
get_mod_stats(): Compute Statistics for a Ch3 File
get_mod_table(): Collect Table from DuckDB Database as Tibble
get_mod_tableinfo(): Get Table Information from mod Database
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)
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
print(<mod_db>): Helper Function to Print Database Tables
remove_mod_table(): Remove a table from a database connection.
rename_mod_samples(): Rename sample names in a table
run_mod_analysis(): Run Differential Analysis on Methylation Data
run_mod_dplyr(): Execute an Expression on a DuckDB Table with Optional Materialization
run_mod_qc(): Quality Control Wrapper for Methylation Data
run_mod_sql(): Execute a query on a mod Database
summarize_mod_positions(): Summarize per-position methylation calls into a DuckDB table
summarize_mod_reads(): Summarize Reads in a Database
summarize_mod_regions(): Summarize methylation by annotated regions
summarize_mod_windows(): Summarize methylation in sliding windows
trim_mod_reads(): Trim methylation calls at the read ends in a mod database