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

Description

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

Usage

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

Arguments

Details

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

Value

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

References

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

See Also

regionSegCost

Examples

	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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(biomvRCNS)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biomvRCNS/regionSegAlphaNB.Rd_%03d_medium.png", width=480, height=480)
> ### Name: regionSegAlphaNB
> ### Title: Estimate matrix of dispersion parameter alpha (size) used in
> ###   'regionSegCost' for negative binomial distributed 'x'.
> ### Aliases: regionSegAlphaNB
> 
> ### ** Examples
> 
> 	x<-matrix(rnbinom(120, size=0.05, mu=20), ncol=3)
> 	Aa<-regionSegAlphaNB(x, maxk=20)
> 	dim(Aa) # [1] 20 40
[1] 20 40
> 	Ab<-regionSegAlphaNB(x, segs=as.integer(c(3, 6, 12, 30)))
> 	dim(Ab) # [1] 5 5
[1] 5 5
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>