Description Objects from the Class Slots Methods Author(s) Examples
COUPLINGset class is used in the MEDIPS library to store and extract information generated during the creation of a coupling vector.
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.
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
signature(object = "COUPLINGset")
: extracts the reference genome of the COUPLING SET
signature(object = "COUPLINGset")
: extracts the window size from the window_size slot COUPLING SET
signature(object = "COUPLINGset")
: extracts the names of the chromosomes included within the COUPLING SET
signature(object = "COUPLINGset")
: extracts the length of the chromosomes included within the COUPLING SET
signature(object = "COUPLINGset")
: extracts the sequence pattern (e.g. CpG)
signature(object = "COUPLINGset")
: extracts the coupling factor at the genomic bins
signature(object = "COUPLINGset")
: extracts the total number of sequence pattern
signature(object = "COUPLINGset")
: prints a summary of the COUPLING SET object content
Lukas Chavez, Matthias Lienhard, Joern Dietrich
1 | showClass("COUPLINGset")
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