geneExprTest {erccdashboard} | R Documentation

## Prepare differential expression testing results for spike-in analysis

### Description

Prepare differential expression testing results for spike-in analysis

### Usage

    geneExprTest(exDat)

### Arguments

`exDat` | list, contains input data and stores analysis results

### Details

This function wraps the QuasiSeq differential expression testing package for datType = "count" or uses the limma package for differential expression testing if datType = "array". Alternatively, for count data only, if correctly formatted DE test results are provided, then geneExprTest will bypass DE testing (with reduced runtime).

### Examples

    data(SEQC.Example)

    exDat <- initDat(datType="array", isNorm=FALSE,
                     exTable=UHRR.HBRR.arrayDat,
                     filenameRoot="testRun", sample1Name="UHRR",
                     sample2Name="HBRR", erccmix="RatioPair",
                     erccdilution = 1, spikeVol = 50,
                     totalRNAmass = 2.5*10^(3), choseFDR=0.01)

    exDat <- est_r_m(exDat)

    exDat <- dynRangePlot(exDat)

    exDat <- geneExprTest(exDat)

[Package erccdashboard version 1.12.1 Index]