maSignal {erccdashboard} | R Documentation

## 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

[Package erccdashboard version 1.12.1 Index]