HiCDOCDataSet
components.R/AllGenerics.R
, R/methods.R
HiCDOCDataSet-methods.Rd
Retrieve information and results from a HiCDOCDataSet
.
chromosomes(object) positions(object) conditions(object) replicates(object) interactions(object) binSize(object) compartments(object) differences(object, threshold = 0.05) concordances(object)
object | a HiCDOCDataSet object |
---|---|
threshold | a numeric value between 0 and 1. If no threshold, all the differences will
be printed even the non significant ones. Otherwise the differences printed
are filtered to show the ones with an adjusted p-value <= |
A character vector (for chromosomes
, conditions
,
replicates
), an integer(for binSize
), a tibble
(for interactions
and positions
), or a GRanges object
(for compartments
, concordances
, differences
).
chromosomes
: Retrieves the vector of chromosome names.
positions
: Retrieves the genomic positions corresponding to bins for each chromosome.
conditions
: Retrieves the vector of condition names.
replicates
: Retrieves the vector of replicate names.
interactions
: Retrieves a tibble of the interactions.
binSize
: Retrieves the resolution (span of each position in number of bases).
compartments
: Retrieves a GenomicRange
of the compartment of every position
in every condition.
differences
: Retrieves a GenomicRange
of the significant compartment differences
between conditions, and their p-values.
concordances
: Retrieves a GenomicRange
of the concordance (confidence in assigned
compartment) of every position in every replicate.
show,HiCDOCDataSet-method
: Describes the object and its methods.
#> [1] "W" "X" "Y" "Z"conditions(exampleHiCDOCDataSet)#> [1] "2" "1" "2" "1" "3" "3" "1"binSize(exampleHiCDOCDataSet)#> [1] 137