edgerDfFromContrasts: Obtain edgeR results from counts, design and contrasts matrix

In martingarrido/biokit: Toolkit for the automatic analysis of omics data

Description

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.

Usage

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.

martingarrido/biokit documentation built on June 27, 2021, 2:21 a.m.