runLimma: Modeling CRISPR screen data by R package limma

In CEDA: CRISPR Screen and Gene Expression Differential Analysis

Modeling CRISPR screen data by R package limma

Description

The lmFit function in R package limma is employed for group comparisons.

Usage

runLimma(data, design, contrast.matrix)

Arguments

data	A numeric matrix containing log2 expression levels of sgRNAs with rows corresponding to sgRNAs and columns corresponding to samples.
design	A design matrix with rows corresponding to samples and columns corresponding to coefficients to be estimated.
contrast.matrix	A matrix with columns corresponding to contrasts.

Value

A data frame with rows corresponding to sgRNAs and columns corresponding to limma results

Examples

y <- matrix(rnorm(1000*6),1000,6)
condition <- gl(2,3,labels=c("Treatment","Baseline"))
design <- model.matrix(~ 0 + condition)
contrast.matrix <- makeContrasts("conditionTreatment-conditionBaseline",levels=design)
limma.fit <- runLimma(y,design,contrast.matrix)

CEDA documentation built on May 29, 2024, 7:44 a.m.