MEAL (version 1.2.3)

DAProbe: Perform per probe analysis

Description

Compute statistics (t estimate and p-value) for methylation or expression data using linear or robust linear regression.

Usage

DAProbe(set, model, coefficient = 2, shrinkVar = FALSE, method = "robust", max_iterations = 100)

Arguments

set

MethylationSet, matrix of M-values or ExpressionSet.

model

Matrix with the model

coefficient

Numeric with the index of the model matrix used to perform the analysis. If a vector is supplied, a list will be returned.

shrinkVar

Logical indicating if shrinkange of variance should be performed.

method

String indicating the method used in the regression ("ls" or "robust")

max_iterations

Numeric indicating the maximum number of iterations done in the robust method.

Value

Data.frame or list of data.frames containing intercept and slope values. If the set is a MethylationSet, probe's position, chromosome and the nearest gene are also returned.

Examples

if (require(minfiData)){
 mvalues <- getM(MsetEx)[1:100, ]
 model <- model.matrix(~ Sample_Group, data = pData(MsetEx)) 
 res <- DAProbe(mvalues, model, method = "ls")
 head(res)
}