Class "GElist"

Description

This class is used in the methylPipe library to collect a set of GEcollection objects

Objects from the Class

Objects can be created by calls of the form new("GElist", ...) or using the function GElist(Objlist,names), see below. GElist are a collection of GEcollection objects (see GElist-class).

Slots

Objlist:

Object of class "list" : a list where each item is a GEcollection object

names:

Object of class "character" : vector of the names of the objects

Methods

"[["

signature(x = "GElist"): subsets the GElist returning a specific GEcollection object

"[[<-"

signature(x = "GElist"): replaces the specific GEcollection object in the GElist

"["

signature(x = "GElist"): subsets the GElist returning another GElist

Author(s)

Mattia Pelizzola

See Also

GElist-class

Examples

gecollect_file <- system.file('extdata', 'gec.H1.Rdata', package='methylPipe')
load(gecollect_file)
gec1 <- gec.H1[start(gec.H1) < 153924]
gec2 <- gec.H1[start(gec.H1) > 153924]
gel.set <- GElist(g1=gec1, g2=gec2)

Results

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> library(methylPipe)
Loading required package: GenomicRanges
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: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methylPipe/GElist-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GElist-class
> ### Title: Class "GElist"
> ### Aliases: GElist-class GElist show,GElist-method length,GElist-method
> ###   [[<-,GElist,ANY,ANY-method [[,GElist,ANY,ANY-method
> ###   [,GElist,ANY,ANY-method $,GElist-method $,GElist
> ### Keywords: classes
> 
> ### ** Examples
> 
> gecollect_file <- system.file('extdata', 'gec.H1.Rdata', package='methylPipe')
> load(gecollect_file)
> gec1 <- gec.H1[start(gec.H1) < 153924]
> gec2 <- gec.H1[start(gec.H1) > 153924]
> gel.set <- GElist(g1=gec1, g2=gec2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>