initDat: Initialize the exDat list

In arcolombo/Rccdashboard: Assess Differential Gene Expression Experiments with ERCC Controls

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)                      
                                        

arcolombo/Rccdashboard documentation built on May 10, 2019, 12:49 p.m.