geneExprTest {erccdashboard} | R Documentation |
Prepare differential expression testing results for spike-in analysis
geneExprTest(exDat)
exDat |
list, contains input data and stores analysis results |
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).
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)