FDRcurve: FDR curves

Description Usage Arguments Value Author(s) Examples

Description

FDR curves is a functions which allow plotting the Real False Discoveries commited as number of differential expressed genes are identified by several hypothesis testing methods, shuch a several Differential Expression analysis.

Usage

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FDRcurve(dataRoc, main)

Arguments

dataRoc

a data.frame where each column stores p values from each of the hypothesis test methods which are wanted to compare. The last column store the information related to real differential expression, where "0" means no differential expression and "1" means differential expression.

main

the title of the plot

Value

a plot with the FDRs curves for every and each one of hypothesis test methods

Author(s)

Enrique Perez_Riesgo

Examples

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library(compcodeR)
library(edgeR)
set.seed(123456987)
datasCI<-generateSyntheticData(dataset = EMOresults, n.vars = 15000,samples.per.cond = 6, n.diffexp = 1500,repl.id = 1, seqdepth = 1e7,fraction.upregulated = 0.5,between.group.diffdisp = FALSE,filter.threshold.total = 1,filter.threshold.mediancpm = 0,fraction.non.overdispersed = 0)
expressiondata<-datasCI@count.matrix
TMMfac<-calcNormFactors.default(expressiondata,method = "TMM")
exprT<-t(t(expressiondata)*TMMfac)
conditions<-(datasCI@sample.annotations$condition-1)
testEMOTMM<-EMObuODlmTest(expr=exprT, condition = conditions,original = exprT,originalm=exprT)
edgeR.dgelist = DGEList(counts = expr, group = factor(conditions))
edgeR.dgelist = calcNormFactors(edgeR.dgelist, method = "TMM")
edgeR.dgelist = estimateCommonDisp(edgeR.dgelist)
edgeR.dgelist = estimateTagwiseDisp(edgeR.dgelist, trend = "movingave")
edgeR.test = exactTest(edgeR.dgelist)
edgeR.pvalues = edgeR.test$table$PValue
edgeR.adjpvalues = p.adjust(edgeR.pvalues, method = "BH")
testedgeRTMM<-data.frame(FC=edgeR.test$table$logFC, PVALUE=edgeR.test$table$PValue, ADJ.PVAL=edgeR.adjpvalues)
dataRoc<-data.frame(EMO=testEMOTMM$ADJ.PVAL,edgeR=testedgeRTMM$ADJ.PVAL, DE=expr3@variable.annotations$differential.expression)
FDRcurve(dataRoc = dataRoc, main="FDR curves")

emodoro/dEMO documentation built on May 28, 2019, 12:57 p.m.