Obtain edgeR results from counts, design and contrasts matrix

Source: R/edger_pairwise_comparison.R

Applies recommended edgeR steps to obtain differential expression tables from an initial count matrix object. As in limmaDfFromContrasts, it uses a design matrix and a contrast matrix as input.

edgerDfFromContrasts(
  counts,
  desMat,
  conMat,
  filterByExpr = FALSE,
  compName = "comparison",
  featName = "feature",
  exprName = "AveExpr",
  fcName = "logFc",
  pName = "pValue",
  pAdjName = "pAdj"
)

Arguments

counts

The count matrix to analyze.
desMat

Design matrix.
conMat

Contrasts matrix.
filterByExpr

Apply filterByExpr?
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.