QQP: The Quantile-Quantile Plot to compare the empirical q's and...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/QQP.R

Description

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

Usage

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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.

Author(s)

Ning Leng

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

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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)

EBSeq documentation built on Nov. 17, 2017, 9:55 a.m.