maSignal: Generate MA plots with or without annotation using LODR...

Description Usage Arguments Examples

View source: R/maSignal.R

Description

Generate MA plots with or without annotation using LODR estimates

Usage

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maSignal(exDat, alphaPoint = 0.8, r_mAdjust = TRUE, replicate = TRUE)

Arguments

exDat

list, contains input data and stores analysis results

alphaPoint

numeric value, for alpha (transparency) for plotted points, range is 0 - 1

r_mAdjust

default is TRUE, if FALSE then the r_m estimate will not used to offset dashed lines for empirical ratios on figure

replicate

default is TRUE, if FALSE then error bars will not be produced

Examples

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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)
# generate MA plot without LODR annotation
exDat <- maSignal(exDat)

exDat$Figures$maPlot

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

# Include LODR annotation
exDat <- annotLODR(exDat)

exDat$Figures$maPlot

erccdashboard documentation built on Oct. 31, 2019, 3:19 a.m.