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

In EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data

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.

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

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. 8, 2020, 6:52 p.m.