DenNHist: Density plot to compare the empirical q's and the simulated...

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

Description

'DenNHist' gives the density plot that compares the empirical q's and the simulated q's from the fitted beta distribution.

Usage

DenNHist(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. The empirical estimation of q's will be represented as blue histograms and the density of the fitted beta distribution will be represented as the green line.

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

beta.mom, QQP, EBTest, EBMultiTest

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))
DenNHist(EBOut)

EBSeq documentation built on Nov. 8, 2020, 6:52 p.m.