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 |