runDiffMeanAnalysis: Run differential mean analysis
In MEAL: Perform methylation analysis

Description Usage Arguments Value Examples

Run differential mean analysis using t-moderated statistics. This function relies on lmFit from limma package.

runDiffMeanAnalysis(
  set,
  model,
  weights = NULL,
  method = "ls",
  max_iterations = 100,
  betas = TRUE,
  resultSet = TRUE,
  warnings = TRUE,
  ...
)

`set`	Matrix, `GenomicRatioSet`, `SummarizedExperiment` or `ExpressionSet`.
`model`	Model matrix or formula to get model matrix from `set`.
`weights`	weights used in the lmFit model.
`method`	String indicating the method used in the regression: "ls" or "robust". (Default: "ls")
`max_iterations`	Numeric indicating the maximum number of iterations done in the robust method.
`betas`	If `set` is a `GenomicRatioSet`, should beta values be used? (Default: TRUE)
`resultSet`	Should results be encapsulated in a `resultSet`? (Default: TRUE)
`warnings`	Should warnings be displayed? (Default:TRUE)

MArrayLM or resultSet with the result of the differential mean analysis.

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