LogN: The function to run EM (one round) algorithm for the NB-beta...
In lengning/EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data
Description
Usage
Arguments
Author(s)
References
Examples
Description
'LogN' specifies the function to run (one round of) the EM algorithm for the NB-beta model.
Usage
1
2
LogN(Input, InputSP, EmpiricalR, EmpiricalRSP, NumOfEachGroup,
AlphaIn, BetaIn, PIn, NoneZeroLength)
Arguments
Input, InputSP
The expressions among all the samples.
NumOfEachGroup
Number of genes in each Ng group.
AlphaIn, PIn, BetaIn, EmpiricalR, EmpiricalRSP
The parameters from the last EM step.
NoneZeroLength
Number of Ng groups.
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
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5
6
#Input = matrix(rnorm(100,100,1), ncol=10)
#rownames(Input) = paste("g",1:10)
#RIn = matrix(rnorm(100,200,1), ncol=10)
#res = LogN(Input, list(Input[,1:5], Input[,6:10]),
# RIn, list(RIn[,1:5], RIn[,6:10]),
# 10, .6, .7, .3, 1)
lengning/EBSeq documentation built on May 21, 2019, 4:02 a.m.
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Description Usage Arguments Author(s) References Examples
Description
'LogN' specifies the function to run (one round of) the EM algorithm for the NB-beta model.
Usage
1 2 | LogN(Input, InputSP, EmpiricalR, EmpiricalRSP, NumOfEachGroup,
AlphaIn, BetaIn, PIn, NoneZeroLength)
|
Arguments
Input, InputSP |
The expressions among all the samples. |
NumOfEachGroup |
Number of genes in each Ng group. |
AlphaIn, PIn, BetaIn, EmpiricalR, EmpiricalRSP |
The parameters from the last EM step. |
NoneZeroLength |
Number of Ng groups. |
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
1 2 3 4 5 6 | #Input = matrix(rnorm(100,100,1), ncol=10)
#rownames(Input) = paste("g",1:10)
#RIn = matrix(rnorm(100,200,1), ncol=10)
#res = LogN(Input, list(Input[,1:5], Input[,6:10]),
# RIn, list(RIn[,1:5], RIn[,6:10]),
# 10, .6, .7, .3, 1)
|
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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