Description Usage Arguments Value Author(s) References Examples
'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.)
1 | GetNg(IsoformName, GeneName, TrunThre = 3)
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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. |
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). |
Ning Leng
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)
1 2 3 4 5 6 7 8 9 10 11 12 | 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)
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