erccdashboard (version 1.6.0)

runDashboard: 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)