smoking_analysis: Replicate smoking analysis of Liu et al. and Hannum et al....

In cozygene/CellTypeSpecificMethylationAnalysis: Evaluation of Cell Type Specific Methylation Analysis

Description

Replicate smoking analysis of Liu et al. and Hannum et al. datasets

Usage

smoking_analysis(
  hannum_smk_status_path,
  data_dir,
  results_dir,
  plot_dir,
  plot_type = "tiff",
  n.sites = NULL
)

Arguments

hannum_smk_status_path	Path to CSV containing GSM IDs as rownames and a column titled smk that contains either Never, Current Smoker, or Past Smoker for each sample.
data_dir	Directory to save Liu and Hannum data for analysis
results_dir	Directory to save results
plot_dir	Directory to save plots
plot_type	Extension for saving plot graphics, such as pdf or png
n.sites	Number of sites to subset from each subset for quick execution (for testing)

Value

A list of results. Slot results contains a list of p-values generated by each method. Slot plot contains plot of results.

cozygene/CellTypeSpecificMethylationAnalysis documentation built on Jan. 28, 2022, 11:20 a.m.