COUPLINGset-class: COUPLINGset class and internal functions

In MEDIPS: DNA IP-seq data analysis

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")

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'BSgenome'

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

    GenomeDescription, bsgenomeName, organism, provider,
    providerVersion, releaseDate, releaseName, species

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

    organism, species

Loading required package: Rsamtools

Attaching package: 'Rsamtools'

The following object is masked from 'package:BiocGenerics':

    path

Warning: namespace 'rtracklayer' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'rtracklayer' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning messages:
1: multiple methods tables found for 'organism' 
2: multiple methods tables found for 'species' 
3: multiple methods tables found for 'seqinfo' 
4: multiple methods tables found for 'seqinfo<-' 
5: multiple methods tables found for 'seqnames' 
6: no function found corresponding to methods exports from 'DelayedArray' for: 'acbind', 'arbind' 
7: no function found corresponding to methods exports from 'SummarizedExperiment' for: 'acbind', 'arbind' 
8: replacing previous import 'BiocGenerics::path' by 'Rsamtools::path' when loading 'GenomicAlignments' 
9: multiple methods tables found for 'rglist' 
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

MEDIPS documentation built on Nov. 8, 2020, 5:05 p.m.