Calculate and Plot Coverage Statistics — plot_mod

This function calculates and optionally plots statistics for coverage data from methylation sequencing experiments. It can handle both positional and regional methylation data.

Usage

plot_mod_cov(
  mod_db,
  call_type = "positions",
  plot = TRUE,
  save_path = NULL,
  max_rows = NULL
)

Arguments

mod_db: A data base either linking to the file name or of class mod_db.
call_type: Either positions or regions data to analyze coverage on.
plot: Logical, if TRUE, the function will generate a histogram of the coverage data. 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 summary statistics and percentiles of the coverage data. If plot is TRUE, it prints a histogram of the log-transformed coverage data.

Examples

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