Class "ExomeCopy"

Description

Object returned by exomeCopy

Objects from the Class

Objects can be created by calls of the form new("ExomeCopy").

Slots

sample.name:

Object of class "character": an identifier for the sample

type:

Object of class "character": the type of model used, either "exomeCopy" or "exomeCopyVar"

path:

Object of class "Rle": the index of the predicted state for each window

ranges:

Object of class "IRangesList": the corresponding ranges for the observed counts and covariates

O.norm:

Object of class "numeric": the input vector of counts divided by X * beta

log.odds:

Object of class "numeric": the log ratio of the emission probabilities along the predicted path over the emission probabilities of the normal state

fx.par:

Object of class "list": a list of the settings S, d, normal.state and fit.var

init.par:

Object of class "list": a list of the initial parameters goto.cnv, goto.normal, beta.hat and phi.hat

final.par:

Object of class "list": a list of the final parameters goto.cnv, goto.normal, beta (and gamma for exomeCopyVar)

counts:

Object of class "numeric": the number of evaluations of the log likelihood performed by optim

convergence:

Object of class "numeric": the integer for convergence of optim, 0 for convergence

nll:

Object of class "numeric": the final value of the negative log likelihood

Methods

plot

signature(x = "ExomeCopy", y = "missing"): ...

show

signature(object = "ExomeCopy"): ...

See Also

exomeCopy

Examples

showClass("ExomeCopy")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(exomeCopy)
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/exomeCopy/ExomeCopy-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ExomeCopy-class
> ### Title: Class "ExomeCopy"
> ### Aliases: ExomeCopy-class plot,ExomeCopy,missing-method
> ###   show,ExomeCopy-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("ExomeCopy")
Class "ExomeCopy" [package "exomeCopy"]

Slots:
                                                                              
Name:  sample.name        type        path      ranges      O.norm    log.odds
Class:   character   character         Rle IRangesList     numeric     numeric
                                                                              
Name:       fx.par    init.par   final.par      counts convergence         nll
Class:        list        list        list     numeric     numeric     numeric
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>