ct.preprocessFit: Preprocess a 'MArrayLM' model fit object to include only one...

In RussBainer/gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Preprocess a 'MArrayLM' model fit object to include only one contrast.

Description

This function preprocesses a fit object returned from eBayes to include only the values relevant to the modelTerm specified.

Usage

ct.preprocessFit(fit, modelTerm)

Arguments

fit	An object of class MArrayLM to be processed.
modelTerm	The model coefficient to be isolated for downstream analyses.

Value

A MArrayLM object for downstream processing.

Author(s)

Russell Bainer

Examples

#Load and preprocess data
data('es')
library(Biobase)
library(limma)

#Make a multi-level contrast
design <- model.matrix(~ 0 + TREATMENT_NAME, pData(es))
colnames(design) <- gsub('TREATMENT_NAME', '', colnames(design))
contrasts <- makeContrasts((ControlExpansion - ControlReference), (DeathExpansion - ControlExpansion), levels = design)

#Make a multi-level fit object
vm <- voom(exprs(es), design)
fit <- lmFit(vm, design)
fit <- contrasts.fit(fit, contrasts)
fit <- eBayes(fit)  

#And trim it
fit2  <- ct.preprocessFit(fit, modelTerm = '(DeathExpansion - ControlExpansion)')

ncol(fit)
ncol(fit2)

RussBainer/gCrisprTools documentation built on Nov. 5, 2022, 2:35 p.m.