maSignal {erccdashboard} | R Documentation |
Generate MA plots with or without annotation using LODR estimates
maSignal(exDat, alphaPoint = 0.8, r_mAdjust = TRUE, replicate = TRUE)
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 |
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