Obtain limma results from data, design and contrasts matrix.

Source: R/limma_pairwise_comparison.R

Creates a linear model with limma and fits it to the provided contrasts. Then uses eBayes to smooth standard errors and obtain the list of pairwise comparison results with topTable.

limmaDfFromContrasts(
  mat,
  desMat,
  conMat,
  trend = FALSE,
  compName = "comparison",
  featName = "feature",
  exprName = "AveExpr",
  fcName = "logFc",
  pName = "pValue",
  pAdjName = "pAdj"
)

Arguments

mat

Matrix with data to analyse.
desMat

Design matrix.
conMat

Contrasts matrix.
trend

logical, should an intensity-trend be allowed for the prior variance? Default is that the prior variance is constant.
compName

Name for the column that indicates the pairwise comparison in the tidy data frame.
featName

Name for the column that indicates the analyzed row feature in the tidy data frame.
exprName

Name for the resulting average expresion column.
fcName

Name for the resulting fold change column.
pName

Name for the resulting p value column.
pAdjName

Name for the resulting adjusted p value column.

Value

A data frame with the results in a tidy format.