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Get Methylation Statistics from the Modifications Database

Source: R/plot_mod_modfrac.R
plot_mod_modfrac.Rd

This function retrieves and calculates methylation statistics (mean methylation fractions) from a specified table in the mod database. It can either return summary statistics or plot a histogram of the methylation values, depending on the user's preference.

Usage

plot_mod_modfrac(
  mod_db,
  call_type = c("positions", "regions"),
  plot = TRUE,
  save_path = NULL,
  max_rows = NULL
)

Arguments

mod_db

A string. The path to the database containing mod files from nanopore data.

call_type

A character vector specifying the type of data to retrieve from the database. Default is "positions". Can also be "regions".

plot

A logical value. If TRUE, a histogram of methylation values is plotted. Default is FALSE.

save_path

Pathway to save the plot to. Usually .pdf or .png.

max_rows

The maximum amount of rows wanted for calculation. This argument can help analysis run faster when there is a lot of data.

Value

If `plot` is FALSE, the function prints a summary of the methylation statistics and quantiles. If `plot` is TRUE, it displays a histogram of methylation values.

Details

The function connects to the specified database, checks for the existence of the relevant table, and retrieves methylation fraction data. If the table contains methylation data, it prioritizes the `mh_frac` column over others. Depending on the `call_type`, it can compute statistics for either per base or per region. If `plot` is set to TRUE, it generates a histogram of the methylation values.

Note

The function assumes that the database has tables named according to the `call_type` parameter (e.g., "positions", "regions"). It also expects specific columns for methylation data to exist.

Examples

 # Specify the path to the database
 mod_db <- system.file("my_data.mod.db", package = "ModSeqR")
 
 # Get methylation statistics for the 'positions' call type without plotting
 plot_mod_modfrac(mod_db = mod_db, call_type = "positions")
#> Error in plot_mod_modfrac(mod_db = mod_db, call_type = "positions"): positions Table does not exist in the database. Check spelling or make sure you create it first.