Beta-Binomial modeling of the overdispersion of the RNA-seq count data


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Documentation for package ‘BBSeq’ version 1.0

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BBSeq-package Beta-Binomial modeling of the overdispersion of the RNA-seq count data
BBSeq Beta-Binomial modeling of the overdispersion of the RNA-seq count data
Beta.free Beta estimation by FREE approach
constrained Get the negative log-likelihood in Constrained Approach
constrained.estimate Beta estimation by FREE approach
constrained.estimate Get the negative log-likelihood in Constrained Approach
constrained.estimate The main function of Constrained approach
constrained.estimate outlier detection function
constrained.estimate psi estimation from FREE approach
data.anno The annotation file for dataset data.Y
data.Y the sample data of this BBSeq package
data.Y The annotation file for dataset data.Y
free.estimate Beta estimation by FREE approach
free.estimate The main function for FREE approach
free.estimate Get the negative log-likelihood by FREE Approach
free.mle get the maximum likelihood matrix
freefunction The main function for FREE approach
freefunction Get the negative log-likelihood by FREE Approach
get.beta.start Find the initial gene-specific staring values for parameters of
get.beta.start Simple linear regression function.
get.psi.start The initial value of the over-dispersion paramter of each gene.
lib.size The main function for FREE approach
lib.size Get negative loglikelihood values
lib.size Get the negative log-likelihood by FREE Approach
lib.size Find the initial gene-specific staring values for parameters of
lib.size The initial value of the over-dispersion paramter of each gene.
like get the maximum likelihood matrix
myoptim.free Get negative loglikelihood values
myoptim.free Optimization function for estimating the gene-specific parameter of
myregression Simple linear regression function.
outlier outlier detection function
outlier.flag flag the suspicious gene
outlier.flag flag the suspicious gene
outlier.total flag the suspicious gene
psi.free psi estimation from FREE approach
regression The main function for FREE approach
regression the linear regression function
X.builder Construct different design matrix with respect to the paramters of