COUPLINGset class and internal functions

Description

COUPLINGset class is used in the MEDIPS library to store and extract information generated during the creation of a coupling vector.

Objects from the Class

Objects of the classes contain information about sequence pattern information, included chromosomes, and further parameter settings. A COUPLING SET object is created by the MEDIPS.couplingVector() function. According slots will be filled during the workflow.

Slots

genome_name:

Object of class "character" : the refernce genome

window_size:

Object of class "numeric" : the window size for the genome vector

chr_names:

Object of class "character" : the names of the chromosomes included within the MEDIPS/COUPLING SET

chr_lengths:

Object of class "numeric" : the lengths of the chromosomes included within the MEDIPS/COUPLING SET

seq_pattern:

Object of class "character" : the sequence pattern (e.g. CG)

genome_CF:

Object of class "numeric" : the coupling factor at the genomic bins

number_pattern:

Object of class "numeric" : the total number of sequence pattern

Methods

genome_name

signature(object = "COUPLINGset"): extracts the reference genome of the COUPLING SET

window_size

signature(object = "COUPLINGset"): extracts the window size from the window_size slot COUPLING SET

chr_names

signature(object = "COUPLINGset"): extracts the names of the chromosomes included within the COUPLING SET

chr_lengths

signature(object = "COUPLINGset"): extracts the length of the chromosomes included within the COUPLING SET

seq_pattern

signature(object = "COUPLINGset"): extracts the sequence pattern (e.g. CpG)

genome_CF

signature(object = "COUPLINGset"): extracts the coupling factor at the genomic bins

number_pattern

signature(object = "COUPLINGset"): extracts the total number of sequence pattern

show

signature(object = "COUPLINGset"): prints a summary of the COUPLING SET object content

Author(s)

Lukas Chavez, Matthias Lienhard, Joern Dietrich

Examples

showClass("COUPLINGset")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(MEDIPS)
Loading required package: BSgenome
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: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MEDIPS/COUPLINGset-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: COUPLINGset-class
> ### Title: COUPLINGset class and internal functions
> ### Aliases: COUPLINGset COUPLINGset-class genome_name,COUPLINGset-method
> ###   window_size,COUPLINGset-method chr_names,COUPLINGset-method
> ###   chr_lengths,COUPLINGset-method seq_pattern,COUPLINGset-method
> ###   genome_CF,COUPLINGset-method number_pattern,COUPLINGset-method
> ###   show,COUPLINGset-method seq_pattern genome_CF number_pattern
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("COUPLINGset")
Class "COUPLINGset" [package "MEDIPS"]

Slots:
                                                                  
Name:     seq_pattern    genome_name      genome_CF number_pattern
Class:      character      character        numeric        numeric
                                                   
Name:     window_size      chr_names    chr_lengths
Class:        numeric      character        numeric
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>