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, 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.

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 May 24, 2018, 6:02 p.m.