EBSeq (version 1.12.0)

QQP: The Quantile-Quantile Plot to compare the empirical q's and simulated q's from fitted beta distribution

Description

'QQP' gives the Quantile-Quantile Plot to compare the empirical q's and simulated q's from fitted beta distribution.

Usage

QQP(EBOut, GeneLevel = F)

Arguments

EBOut

The output of EBTest or EBMultiTest.

GeneLevel

Indicate whether the results are from data at gene level.

Value

For data with n1 conditions and n2 uncertainty groups, n1*n2 plots will be generated. Each plot represents a subset of the data.

References

Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M.G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, and Christina Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (2013)

See Also

EBTest, EBMultiTest, DenNHist

Examples

data(GeneMat)
GeneMat.small = GeneMat[c(500:1000),]
Sizes = MedianNorm(GeneMat.small)
EBOut = EBTest(Data = GeneMat.small,
	Conditions = as.factor(rep(c("C1","C2"), each=5)),
	sizeFactors = Sizes, maxround = 5)
par(mfrow=c(2,2))
QQP(EBOut)