Class "biomvRCNS"

Description

The default object class returned by biomvRhsmm, biomvRseg and biomvRmgmr

Objects from the Class

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

Slots

x:

Object of class "GRanges", with range information either from real positional data or just indices, with input data matrix stored in the meta columns. Additional meta columns for the estimated states and associated probabilities for each sample will also be appended following the input data matrix when using biomvRhsmm.

res:

Object of class "GRanges" , each range represent one continuous segment identified, with sample name slot 'SAMPLE' and segment mean slot 'MEAN' stored in the meta columns

param:

Object of class "list", list of all parameters used in the corresponding model.

Methods

plot

signature(x = "biomvRCNS", y = "ANY"): ...

show

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

Examples

showClass("biomvRCNS")

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/biomvRCNS-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: biomvRCNS-class
> ### Title: Class '"biomvRCNS"'
> ### Aliases: biomvRCNS-class plot,biomvRCNS,ANY-method
> ###   show,biomvRCNS-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("biomvRCNS")
Class "biomvRCNS" [package "biomvRCNS"]

Slots:
                              
Name:        x     res   param
Class: GRanges GRanges    list
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>