runDiffVarAnalysis: Run differential variance analysis

In MEAL: Perform methylation analysis

Description

Run differential variance analysis. This analysis can only be run with categorical variables. This function relies on varFit from missMethyl package.

Usage

runDiffVarAnalysis(
  set,
  model,
  coefficient = NULL,
  resultSet = TRUE,
  betas = TRUE,
  warnings = TRUE,
  ...
)

Arguments

set	Matrix, GenomicRatioSet, SummarizedExperiment or ExpressionSet.
model	Model matrix or formula to get model matrix from set.
coefficient	Numeric with the coefficients used to make the groups. If NULL, all possible groups will be computed.
resultSet	Should results be encapsulated in a resultSet? (Default: TRUE)
betas	If set is a GenomicRatioSet, should beta values be used? (Default: TRUE)
warnings	Should warnings be displayed? (Default:TRUE)
...	Further arguments passed to varFit.

Value

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

Examples

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

MEAL documentation built on Feb. 3, 2021, 2 a.m.