runDashboard {erccdashboard} | R Documentation

## Run default erccdashboard analysis of ERCC control ratio mixtures

### Description

Run default erccdashboard analysis of ERCC control ratio mixtures

### Usage

    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)

### Arguments

`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

### Examples

    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)

[Package erccdashboard version 1.14.0 Index]