estLODR {erccdashboard} | R Documentation

## 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

[Package erccdashboard version 1.12.1 Index]