ct.preprocessFit {gCrisprTools} | R Documentation

## 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)

[Package gCrisprTools version 1.12.0 Index]