erccdashboard (version 1.6.0)

estLODR: Estimate Limit of Detection of Ratios (LODR)

Description

Estimate Limit of Detection of Ratios (LODR)

Usage

estLODR(exDat, kind = "ERCC", prob = 0.9)

Arguments

exDat

list, contains input data and stores analysis results

kind

"ERCC" or "Sim"

prob

probability, ranging from 0 - 1, default is 0.9

Details

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.

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)

exDat <- estLODR(exDat, kind = "ERCC", prob = 0.9)

exDat$Figures$lodrERCCPlot