initDat {erccdashboard} | R Documentation

## Initialize the exDat list

### Description

Initialize the exDat list

### Usage

    initDat(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" or "array", unnormalized data is expected (normalized data may be accepted in future version of the package). Default is "count" (integer count data),"array" is unnormalized fluorescent intensities from microarray fluorescent intensities (not log transformed or normalized)
`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 counts 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 , default is 0.05
`ratioLim` | Limits for ratio axis on MA plot, default is c(-4,4)
`signalLim` | Limits for signal axis on dynamic range 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 <- initDat(datType="count", isNorm = FALSE, exTable=MET.CTL.countDat,
                     filenameRoot = "testRun",sample1Name = "MET",
                     sample2Name = "CTL", erccmix = "RatioPair",
                     erccdilution = 1/100, spikeVol = 1, totalRNAmass = 0.500,
                     choseFDR = 0.1)
    summary(exDat)

[Package erccdashboard version 1.16.1 Index]