regionSegAlphaNB: Estimate matrix of dispersion parameter alpha (size) used in...
In biomvRCNS: Copy Number study and Segmentation for multivariate biological data

Description Usage Arguments Details Value References See Also Examples

Estimate matrix of dispersion parameter alpha (size) used in regionSegCost for negative binomial distributed x.

1	regionSegAlphaNB(x, maxk = NULL, segs = NULL, useMC = FALSE, tol=1e-06)

`x`	The input data matrix or vector
`maxk`	Maximum number of index to search forward
`segs`	Starting indices (excluding 1) for the candidate segments, for the second stage model, `maxk` will be overridden with `length(segs)+1`.
`useMC`	TRUE if `mclapply` should be used to speed up the calculation
`tol`	tolerance level for the convergence criteria in the maximum likelihood estimation of negative binomial distribution dispersion parameter.

Estimate matrix of dispersion parameter alpha (size) used in regionSegCost for negative binomial distributed x.

Matrix with maxk rows and nrow(x) columns, or a length(segs)+1 square matrix for the second stage model.

Piegorsch, W. W. (1990). Maximum likelihood estimation for the negative binomial dispersion parameter. Biometrics, 863-867.

Robinson MD and Smyth GK (2008). Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 9, 321-332

regionSegCost

	x<-matrix(rnbinom(120, size=0.05, mu=20), ncol=3)
	Aa<-regionSegAlphaNB(x, maxk=20)
	dim(Aa) # [1] 20 40
	Ab<-regionSegAlphaNB(x, segs=as.integer(c(3, 6, 12, 30)))
	dim(Ab) # [1] 5 5