Methods to access a HiCDOCDataSet components.

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)

Arguments

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 <= threshold.

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).

Functions

• 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.

Examples

data(exampleHiCDOCDataSet)
chromosomes(exampleHiCDOCDataSet)
#> [1] "W" "X" "Y" "Z"
conditions(exampleHiCDOCDataSet)
#> [1] "2" "1" "2" "1" "3" "3" "1"
binSize(exampleHiCDOCDataSet)
#> [1] 137