discovery.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/methods_bundeling.R
\name{discovery}
\alias{discovery}
\title{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 \code{discovery} objects may also contain
  useful metadata on the analysis that was run, such as which resolution was
  used. For details on a particular \code{discovery} class, please consult 
  the documentation of the functions that generate the class.

  Functions that generate \code{discovery} objects are the following:
  \describe{ \item{\code{\link[GENOVA]{PESCAn}}}{\code{PESCAn_discovery}
  objects} \item{\code{\link[GENOVA]{APA}}}{\code{APA_discovery} objects}
  \item{\code{\link[GENOVA]{ATA}}}{\code{ATA_discovery} objects}
  \item{\code{\link[GENOVA]{ARA}}}{\code{ARA_discovery} objects}
  \item{\code{\link[GENOVA]{RCP}}}{\code{RCP_discovery} objects}
  \item{\code{\link[GENOVA]{compartment_score}}}{\code{CS_discovery} objects}
  \item{\code{\link[GENOVA]{saddle}}}{\code{saddle_discovery} objects}
  \item{\code{\link[GENOVA]{insulation_score}}}{\code{IS_discovery} objects}
  \item{\code{\link[GENOVA]{insulation_domainogram}}}{\code{domainogram_discovery}
   objects}
  \item{\code{\link[GENOVA]{virtual_4C}}}{\code{virtual4C_discovery} objects}
  \item{\code{\link[GENOVA]{direct_index}}}{\code{DI_discovery} objects}
  \item{\code{\link[GENOVA]{intra_inter_TAD}}}{\code{IIT_discovery} objects}}
}
\section{Operations}{
 \subsection{Subsetting}{\code{discovery} objects can be
  subsetted by using \code{subset(discovery, i)} wherein \code{i} is an
  \code{integer} or \code{character} corresponding to the intended
  sample(s).} \subsection{Combining}{\code{discovery} objects of the same
  type can be combined by using \code{\link[GENOVA]{bundle}(discovery_A,
  discovery_B)}. Generally, discovery objects generated from different
  resolutions or specific to a particular genomic region can not be
  combined.} \subsection{Splitting}{\code{discovery} objects can be split to
  individual samples by using \code{\link[GENOVA]{unbundle}(discovery)}.}
  \subsection{Visualisation}{\code{discovery} objects can be visualised with
  ggplot2 using \code{\link[GENOVA]{visualise}(discovery)}. Alternatively,
  the different discovery types also have base R plotting methods by using
  \code{plot(discovery)}.} \subsection{Quantification}{\code{discovery}
  objects can be quantified using \code{\link[GENOVA]{quantify}(discovery)}}
}