COUPLINGset-class: COUPLINGset class and internal functions

In HPCBio/MEDIPS-BioC: 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")

HPCBio/MEDIPS-BioC documentation built on May 30, 2019, 12:44 p.m.