GetNg {EBSeq} | R Documentation

## Ng Vector

### Description

'GetNg' generates the Ng vector for the isoform level data. (While using the number of isoform in the host gene to define the uncertainty groups.)

### Usage

    GetNg(IsoformName, GeneName, TrunThre = 3)

### Arguments

`IsoformName` | A vector contains the isoform names.
`GeneName` | The gene names of the isoforms in IsoformNames (Should be in the same order).
`TrunThre` | The number of uncertainty groups the user wish to define. The default is 3.

### Value

`GeneNg` | The number of isoforms that are contained in each gene.
`GeneNgTrun` | The truncated Ng of each gene. (The genes contain more than 3 isoforms are with Ng 3.)
`IsoformNg` | The Ng of each isoform.
`IsoformNgTrun` | The truncated Ng of each isoform (could be used to define the uncertainty group assignment).

### 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)

### Examples

    data(IsoList)

    IsoMat = IsoList$IsoMat
    IsoNames = IsoList$IsoNames
    IsosGeneNames = IsoList$IsosGeneNames
    IsoSizes = MedianNorm(IsoMat)
    NgList = GetNg(IsoNames, IsosGeneNames)

    #IsoNgTrun = NgList$IsoformNgTrun
    #IsoEBOut = EBTest(Data = IsoMat, NgVector = IsoNgTrun,
    #	Conditions = as.factor(rep(c("C1","C2"), each=5)),
    #	sizeFactors = IsoSizes, maxround = 5)

[Package EBSeq version 1.30.0 Index]