GetAllPaths: Obtain all possible gene paths for an RNA-seq experiments...
In lengning/EBSeqHMM: Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Obtain all possible gene paths for an RNA-seq experiments
with ordered conditions
Usage
1
GetAllPaths(EBSeqHMMOut, OnlyDynamic=TRUE)
Arguments
EBSeqHMMOut
output from EBSeqHMMTest function
OnlyDynamic
if specifies as TRUE, only dynamic
paths will be shown
Details
GetAllPaths() function may be used to generate all possible
expression paths of a particular design.
Value
output: a vector of paths. For example, Up-Up-Up-Up,
Up-Up-EE-EE, Up-Down-Up-EE, etc.
Author(s)
Ning Leng
Examples
1
2
3
4
5
6
7
data(GeneExampleData)
CondVector <- rep(paste("t",1:5,sep=""),each=3)
Conditions <- factor(CondVector, levels=c("t1","t2","t3","t4","t5"))
Sizes <- MedianNorm(GeneExampleData)
EBSeqHMMGeneOut <- EBSeqHMMTest(Data=GeneExampleData, sizeFactors=Sizes, Conditions=Conditions,
UpdateRd=2)
AllPaths <- GetAllPaths(EBSeqHMMGeneOut)
lengning/EBSeqHMM documentation built on May 21, 2019, 4:02 a.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
Obtain all possible gene paths for an RNA-seq experiments with ordered conditions
Usage
1 | GetAllPaths(EBSeqHMMOut, OnlyDynamic=TRUE)
|
Arguments
EBSeqHMMOut |
output from EBSeqHMMTest function |
OnlyDynamic |
if specifies as TRUE, only dynamic paths will be shown |
Details
GetAllPaths() function may be used to generate all possible expression paths of a particular design.
Value
output: a vector of paths. For example, Up-Up-Up-Up, Up-Up-EE-EE, Up-Down-Up-EE, etc.
Author(s)
Ning Leng
Examples
1 2 3 4 5 6 7 | data(GeneExampleData)
CondVector <- rep(paste("t",1:5,sep=""),each=3)
Conditions <- factor(CondVector, levels=c("t1","t2","t3","t4","t5"))
Sizes <- MedianNorm(GeneExampleData)
EBSeqHMMGeneOut <- EBSeqHMMTest(Data=GeneExampleData, sizeFactors=Sizes, Conditions=Conditions,
UpdateRd=2)
AllPaths <- GetAllPaths(EBSeqHMMGeneOut)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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