dEMO: Differential Expression and confidencial estimation for FC

Description Usage Arguments Details Value Author(s) Examples

This function provides a confidencial interval estimation from log2(proportions ratio) or log2(FC) where proportions belong to negative binomial population, such as RNA-seq data sets. Overdispersion estimation is carried out with estimateTagwiseDisp.default function.

1 2	dEMOODci(expr, condition, original = NULL, alpha = 0.05, method.adj = "BH")

`expr`	data.frame, ExpressionSet or matrix after dataset has been filtered
`condition`	Binary vector where 0 means control and 1 treatment
`original`	data.frame, ExpressionSet or matrix before dataset has been filtered
`alpha`	significance level for hypothesis test. Default value is 0.05
`method.adj`	It is the multiple testing correction method. Default value correspond to Benjamini-Hochberg correction. c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none")

function EMObuODlmTest is employed when data sets came from RNA-seq assays, where each row from expression matrix from RNA-seq data sets are dependent to the other rows into the same column (sample). Conversely, data sets store several rows where each of them does not came from the same experiment, that is, each row has nothing to do with the other rows, and dEMOOD1sci function has to be used.

A data.frame is returned, which cointains log2FC, PVALUE, ADJ.PVAL (adjusted p value) and dEMO.STAT (statistic of dEMO test)

Enrique Perez_Riesgo

datasCI <- compcodeR::generateSyntheticData(dataset = dEMOresults,
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 <- edgeR::calcNormFactors.default(expressiondata, method = "TMM")
exprT <- t(t(expressiondata)*TMMfac)
conditions <- datasCI@sample.annotations$condition
testdEMOODci <- dEMOODci(expr = exprT, condition = (conditions-1),original = exprT)