GetNg: Ng Vector

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

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)

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