discovery: Discovery class

In robinweide/GENOVA: GENOVA: expore the Hi-C

Discovery class

Description

The discovery classes contains the results of the analysis functions within GENOVA. Each discovery object is a list with the data as list-elements and each discovery object has attributes that may be relevant to downstream functions.

Details

Next to the results, the discovery objects may also contain useful metadata on the analysis that was run, such as which resolution was used. For details on a particular discovery class, please consult the documentation of the functions that generate the class.

Functions that generate discovery objects are the following:

PESCAn

PESCAn_discovery objects

APA

APA_discovery objects

ATA

ATA_discovery objects

ARA

ARA_discovery objects

RCP

RCP_discovery objects

compartment_score

CS_discovery objects

saddle

saddle_discovery objects

insulation_score

IS_discovery objects

insulation_domainogram

domainogram_discovery objects

virtual_4C

virtual4C_discovery objects

direct_index

DI_discovery objects

intra_inter_TAD

IIT_discovery objects

Operations

Subsetting

discovery objects can be subsetted by using subset(discovery, i) wherein i is an integer or character corresponding to the intended sample(s).

Combining

discovery objects of the same type can be combined by using bundle(discovery_A, discovery_B). Generally, discovery objects generated from different resolutions or specific to a particular genomic region can not be combined.

Splitting

discovery objects can be split to individual samples by using unbundle(discovery).

Visualisation

discovery objects can be visualised with ggplot2 using visualise(discovery). Alternatively, the different discovery types also have base R plotting methods by using plot(discovery).

Quantification

discovery objects can be quantified using quantify(discovery)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.