DenNHist {EBSeq} | R Documentation

## Density plot to compare the empirical q's and the simulated q's from the fitted beta distribution.

### 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)

[Package EBSeq version 1.32.0 Index]