TIerror: Type I error

Description Usage Arguments Value Author(s) Examples

Description

TIerror is a functions which allow plotting the type I error commited by several hypothesis testing methods, shuch a several Differential Expression analysis.

Usage

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TIerror(dataRoc, resample = 100, 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.

resample

The number of resamplings of genes from data set in order to construct a boxplot from several samples from just one data set. Default value is 100.

main

the title of the plot

Value

a box plot with the Type I error 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)
TIerror(dataRoc = dataRoc, resample=100, main="Type I Error")

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