permuteLimma {CEDA}

Modeling CRISPR data with a permutation test between conditions by R package limma

Description

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

Usage

permuteLimma(data, design, contrast.matrix, nperm)

Arguments

data

A numeric matrix containing log2 expression level of sgRNAs with rows corresponding to sgRNAs and columns to samples.

design

A design matrix with rows corresponding to samples and columns to coefficients to be estimated.

contrast.matrix

A matrix with columns corresponding to contrasts.

nperm

Number of permutations

Value

A numeric matrix containing log2 fold changes with permutations

Examples

y <- matrix(rnorm(1000*6),1000,6)
condition <- gl(2,3,labels=c("Control","Baseline"))
design <- model.matrix(~ 0 + condition)
contrast.matrix <- makeContrasts("conditionControl-conditionBaseline",levels=design)
fit <- permuteLimma(y,design,contrast.matrix,20)