runDashboard {erccdashboard} | R Documentation |
Run default erccdashboard analysis of ERCC control ratio mixtures
runDashboard(datType = NULL, isNorm = FALSE, exTable = NULL, repNormFactor = NULL, filenameRoot = NULL, sample1Name = NULL, sample2Name = NULL, erccmix = "RatioPair", erccdilution = 1, spikeVol = 1, totalRNAmass = 1, choseFDR = 0.05, ratioLim = c(-4, 4), signalLim = c(-14, 14), userMixFile = NULL)
datType |
type is "count" (RNA-Seq) or "array" (microarray), "count" is unnormalized integer count data (normalized RNA-Seq data will be accepted in an updated version of the package), "array" can be normalized or unnormalized fluorescent intensities from a microarray experiment. |
isNorm |
default is FALSE, if FALSE then the unnormalized input data will be normalized in erccdashboard analysis. If TRUE then it is expected that the data is already normalized |
exTable |
data frame, the first column contains names of genes or transcripts (Feature) and the remaining columns are expression measures for sample replicates spiked with ERCC controls |
repNormFactor |
optional vector of normalization factors for each replicate, default value is NULL and 75th percentile normalization will be applied to replicates |
filenameRoot |
string root name for output files |
sample1Name |
string name for sample 1 in the gene expression experiment |
sample2Name |
string name for sample 2 in the gene expression experiment |
erccmix |
Name of ERCC mixture design, "RatioPair" is default, the other option is "Single" |
erccdilution |
unitless dilution factor used in dilution of the Ambion ERCC spike-in mixture solutions |
spikeVol |
volume in microliters of diluted ERCC mix spiked into the total RNA samples |
totalRNAmass |
mass in micrograms of total RNA spiked with diluted ERCC mixtures |
choseFDR |
False Discovery Rate for differential expression testing |
ratioLim |
Limits for ratio axis on MA plot, default is c(-4,4) |
signalLim |
Limits for ratio axis on MA plot, default is c(-14,14) |
userMixFile |
optional filename input, default is NULL, if ERCC control ratio mixtures other than the Ambion product were used then a userMixFile can be used for the analysis |
data(SEQC.Example) exDat <- runDashboard(datType = "count",isNorm = FALSE, exTable = MET.CTL.countDat, filenameRoot = "COH.ILM", sample1Name = "MET", sample2Name = "CTL", erccmix = "RatioPair", erccdilution = 1/100, spikeVol = 1, totalRNAmass = 0.500,choseFDR = 0.1) summary(exDat)