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 |