erccdashboard (version 1.6.0)

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

Description

Generate MA plots with or without annotation using LODR estimates

Usage

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

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