runDiffMeanAnalysis: Run differential mean analysis

In isglobal-brge/MEAL: Perform methylation analysis and facilitates differential expression analyses

Description

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

Usage

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

Arguments

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)

Value

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

Examples

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

isglobal-brge/MEAL documentation built on May 8, 2021, 8:05 p.m.