run_smoking_analysis: Smoking analysis of methylation data

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

Description

Performs cell-type-specific analysis of blood methylation data in the context of smoking. Provides p-values estimated by CellDMC and TCA while correcting for known covariates as well unknown technical variation using PCs calculated from control probes. Combines cell types into myeloid and lymphoid compartments for analysis.

Usage

run_smoking_analysis(X, smk, C1, C2, W, smoking_cpgs, dataset.name)

Arguments

X	Methylation values in matrix with sites as rows and samples as columns
smk	Smoking status encoded as 0 (non-smoker), 1 (ex-smoker), or 2 (smoker) in a matrix with rownames as samples and 1 column entitled smoking
C1	Covariates in matrix format; for covariates that may affect methylation at the cell-type level. Rownames are samples and column names are covariate names
C2	Covariates in matrix format; for covariates that may affect the methylation mixtures. Rownames are samples and column names are covariate names
W	Cell fractions in a matrix with cell types as column names and samples as row names. Expects cell types: "Neutro","Eosino","Mono","CD4T","CD8T","B","NK"
smoking_cpgs	List of CpG names to analyze for associations
dataset.name	Name of dataset for naming output variables.

Value

A list of results. Each slot contains p-values output by each method

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