limmaDfFromContrasts: Obtain limma results from data, design and contrasts matrix.

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

Description

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.

Usage

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.

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