COUPLINGset-class: COUPLINGset class and internal functions

Description Objects from the Class Slots Methods Author(s) Examples

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

1
showClass("COUPLINGset")

MEDIPS documentation built on May 2, 2018, 4:17 a.m.