Usage
MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)
Arguments
data
the RNA-seq data, should be the output from RNASeq.Data
nK
the number of components in MGN. When testing for fold-changes (FC), nK includes all components, when testing for differential expression (DE), nK only includes the components that are NOT degenerated.
p0
the proportion of null genes when testing for DE genes.
d0
the point where 'delta' is degerated, default is 0 when testing for DE genes.
nK0
the number of components that are degenerated when testing for DE genes.
iter.max
maximium number of interations in the EM algorithm
print.steps
print the esimates of MGN in each iteration step, if TRUE. Default is FALSE
MGN0
The initialization of the MGN.
It should be a data.frame with 5 columns: pr, alpha, beta, mu, sigma.
The methods of moment estimation will be used if not provided.
model
data model, can be 'nbinom' or 'poisson'. the default will be the same as in 'data'
nMC
the number of random samples from Gamma and Normal distrubitons in the Monte-Carlo simulation.