Quality Control Wrapper for Methylation Data

This function serves as a wrapper for various quality control analyses on methylation data. It sequentially calculates coverage statistics, modification statistics, correlation analysis, and performs principal component analysis (PCA).

Usage

run_mod_qc(
  mod_db,
  call_type = "positions",
  plot = TRUE,
  max_rows = NULL,
  value = m_frac
)

Arguments

mod_db

A database connection or object containing methylation data.

call_type

A character string indicating the type of call to retrieve data (e.g., "positions", "regions").

plot

Logical; whether to generate plots. Defaults to TRUE.

max_rows

Optional maximum number of rows to use (sampling) for speed on large datasets.

value

Column to use for analyses that take a value input (e.g., correlations/PCA). Accepts a bare column name or a string. Default: m_frac.

Value

Invisibly returns nothing; produces plots and console output.

Examples

if (FALSE) { # \dontrun{
 mod_db <- system.file("my_data.mod.db", package = "MethylSeqR")
 run_mod_qc(mod_db, call_type = "positions")                 # uses m_frac
 run_mod_qc(mod_db, call_type = "regions", value = mh_frac)  # use mh_frac
} # }