estLODR {erccdashboard} | R Documentation |
Estimate Limit of Detection of Ratios (LODR)
estLODR(exDat, kind = "ERCC", prob = 0.9)
exDat |
list, contains input data and stores analysis results |
kind |
"ERCC" or "Sim" |
prob |
probability, ranging from 0 - 1, default is 0.9 |
This is the function to estimate a limit of detection of ratios (LODR) for a a chosen probability and threshold p-value for the fold changes in the ERCC control ratio mixtures.
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) exDat <- estLODR(exDat, kind = "ERCC", prob = 0.9) exDat$Figures$lodrERCCPlot