All functions

CuzickEdwards()

Cuzzick and Edward test

DESeq2paired()

DESeq2 with paired design

DiggleMorrisMorton()

Diggle, Morris and Morton-Jones test

RandomLabelling()

MonteCarlo p-value for Random labelling hypothesis for gene point process

chooseOrness()

Choosing an orness

comp.profiles()

Comparative plot of the randomization p-values

diffMeanTail()

Difference between the means in the tails per column

diggle90()

diggle90 Method proposed in Diggle (1990)

doIt()

Analyzing the p-values

.Lgrneg()

Auxiliary function for diggle90

.Lneg()

Auxiliary function for diggle90

edgeRpaired()

edgeR with paired design

evalOrness()

Plots the original p-values of within pairs comparison

fuller()

OWA weigths using Fuller's method

justDo()

Function to simulation study

justDo2()

Function to simulation study

marginal.analysis()

Generation of randomization p-values

null.paired()

Randomization null distributions for paired designs

oddsratio.p()

p-value for odds-ratio equal 1 for comparing paired counts (RNA-seq,...)

oddsratio.paired()

statistic or p-value for odds-ratio equal 1 for comparing paired counts (RNA-seq,...)

oddsratio.stats()

stats for odds-ratio equal 1 for comparing paired counts (RNA-seq,...)

omicf()

p-values and orness using the owa-randomization procedure

owa.weights()

Calculation of weights for OWA aggregation

p.orness()

Calculation of the p-values for different ornesses

pairedCounts()

Differential expression for counts using ordered weighted averages

proportion.p()

Testing equal proportions for comparing paired counts (RNA-seq,...)

rPairedNB()

Random paired counts using independent negative binomial distributions

rPairedPoisson()

Random paired counts using Poisson distributions

rowtest0()

Tests per row (feature) for marginal differential expression