runDiffMeanAnalysis: Run differential mean analysis

Description Usage Arguments Value Examples

View source: R/runDiffMeanAnalysis.R

Description

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

Usage

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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

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

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