DMP_limma: Detect differentially methylated positions in the DNA using...

In GregoireCoppens/LICMEpigenetics: Processing of Epigenetic data

Detect differentially methylated positions in the DNA using the limma package.

Description

This function first uses the 'lmfit' function from the 'limma' package with methylset and the generated design matrix as its inputs. Next it uses the 'contrast.fit' function from the 'limma' package with the 'lmfit' output and the generated contrast matrix as its inputs. The contrast matrix specifies the comparison of interest (e.g.: Patients vs Controls). To compute a moderated t-statistic of differential expression, it uses empirical Bayes moderation of the standard error.

Usage

DMP_limma(
  set,
  Patient_info,
  cat_vars = NULL,
  cont_vars = NULL,
  Group = NULL,
  confint = TRUE
)

Arguments

set	Preprocessed methylation set, can be genomic methyl set or genomic ratio set.
Patient_info	Data frame with adjustment variables.
cat_vars	The variable names in Patient_info that are categorical variables
cont_vars	The variable names in Patient_info that are continuous variables
Group	The variable in Patient_info that represents which observations belong to which groups
confint	To enable confidence interval for the logFC, set to TRUE or change to CI range.

Value

A list with limma output variables and temporary results

• DMPresult - Data table with statistics per CpG sites

• model - eBayes fitted linear model

• design - Design matrix

• contMatrix - Contrast matrix

• Sign_CpG - CpG names of DMPs

GregoireCoppens/LICMEpigenetics documentation built on April 24, 2023, 10:02 a.m.