getRefLimma {ivygapSE} | R Documentation

## provide access to a limma analysis of RNA-seq profiles for reference histology samples

### Description

provide access to a limma analysis of RNA-seq profiles for reference histology samples

### Usage

    getRefLimma()

### Value

an instance of `MArrayLM-class` representing regularized gene-wise ANOVAs

### Note

Uses `download.file` to acquire RDS of the output of `eBayes` from a public S3 bucket. The limma model was fit using `duplicateCorrelation` to address multiplicity of contributions per donor. Comparisons are to samples labeled `CT-reference` (cellular tumor, reference contributions), with coefficients 2-5 corresponding to CT-mvp (microvascular proliferation), CT-pan (pseudopalisading cells around necrosis), IT (infiltrating tumor), and LE (leading edge), respectively.

### Examples

    requireNamespace("limma")
    ebout = getRefLimma() # is result of eBayes
    colnames(ebout$coef)
    limma::topTable(ebout,2)

[Package ivygapSE version 1.6.0 Index]