geneExprTest: Prepare differential expression testing results for spike-in...

In usnistgov/erccdashboard_preBioC: Assess Differential Gene Expression Experiments with ERCC Controls

Description

Prepare differential expression testing results for spike-in analysis

Usage

geneExprTest(exDat)

Arguments

exDat

list, contains input data and stores analysis results

Details

This function wraps the QuasiSeq differential expression testing package for datType = "count" or uses the limma package for differential expression testing if datType = "array". Alternatively, for count data only, if correctly formatted DE test results are provided, then geneExprTest will bypass DE testing (with reduced runtime).

Examples

data(SEQC.Example)

exDat <- initDat(datType="array", isNorm=FALSE,
                 exTable=UHRR.HBRR.arrayDat,
                 filenameRoot="testRun", sample1Name="UHRR",
                 sample2Name="HBRR", erccmix="RatioPair",
                 erccdilution = 1, spikeVol = 50,
                 totalRNAmass = 2.5*10^(3), choseFDR=0.01)

exDat <- est_r_m(exDat)

exDat <- dynRangePlot(exDat)

exDat <- geneExprTest(exDat)

usnistgov/erccdashboard_preBioC documentation built on May 3, 2019, 2:38 p.m.