estLODR: Estimate Limit of Detection of Ratios (LODR)

In erccdashboard: Assess Differential Gene Expression Experiments with ERCC Controls

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

erccdashboard documentation built on Nov. 8, 2020, 5:50 p.m.