WellHandle.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/WellHandle.R
\name{WellHandle}
\alias{WellHandle}
\title{WellHandle}
\description{
Object for handling database operations related to the storage and 
retrieval of Well objects.
}
\section{Public fields}{
\if{html}{\out{<div class="r6-fields">}}
\describe{
\item{\code{dbConnection}}{A dbConnection object}
}
\if{html}{\out{</div>}}
}
\section{Methods}{
\subsection{Public methods}{
\itemize{
\item \href{#method-WellHandle-new}{\code{WellHandle$new()}}
\item \href{#method-WellHandle-get_by_id}{\code{WellHandle$get_by_id()}}
\item \href{#method-WellHandle-get_all_by_plate}{\code{WellHandle$get_all_by_plate()}}
\item \href{#method-WellHandle-get_replicates}{\code{WellHandle$get_replicates()}}
\item \href{#method-WellHandle-get_all_by_compound}{\code{WellHandle$get_all_by_compound()}}
\item \href{#method-WellHandle-store}{\code{WellHandle$store()}}
\item \href{#method-WellHandle-clone}{\code{WellHandle$clone()}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-WellHandle-new"></a>}}
\if{latex}{\out{\hypertarget{method-WellHandle-new}{}}}
\subsection{Method \code{new()}}{
Create an object for handling database operations related to 
the storage and retrieval of Well objects.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{WellHandle$new(dbConnection = NA)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{dbConnection}}{A dbConnection object}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-WellHandle-get_by_id"></a>}}
\if{latex}{\out{\hypertarget{method-WellHandle-get_by_id}{}}}
\subsection{Method \code{get_by_id()}}{
Retrieve a Well object using its database ID
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{WellHandle$get_by_id(plateID, position)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{plateID}}{Database ID of the Plate object the well belongs to}

\item{\code{position}}{Position of the well in the plate}
}
\if{html}{\out{</div>}}
}
\subsection{Returns}{
A Well object
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-WellHandle-get_all_by_plate"></a>}}
\if{latex}{\out{\hypertarget{method-WellHandle-get_all_by_plate}{}}}
\subsection{Method \code{get_all_by_plate()}}{
Retrieve all wells belonging to the same plate
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{WellHandle$get_all_by_plate(plate)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{plate}}{A Plate object}
}
\if{html}{\out{</div>}}
}
\subsection{Returns}{
List of Well objects
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-WellHandle-get_replicates"></a>}}
\if{latex}{\out{\hypertarget{method-WellHandle-get_replicates}{}}}
\subsection{Method \code{get_replicates()}}{
Retrieve replicates of the given well. A replicate is a well
from the same screen and with same samples and compounds (at the same 
dose and unit).
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{WellHandle$get_replicates(well)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{well}}{A Well object}
}
\if{html}{\out{</div>}}
}
\subsection{Returns}{
List of Well objects
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-WellHandle-get_all_by_compound"></a>}}
\if{latex}{\out{\hypertarget{method-WellHandle-get_all_by_compound}{}}}
\subsection{Method \code{get_all_by_compound()}}{
Retrieve all wells where a compound is found
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{WellHandle$get_all_by_compound(compound, screen = NULL)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{compound}}{A Compound object}

\item{\code{screen}}{(optional) a Screen object to limit to wells from this screen}
}
\if{html}{\out{</div>}}
}
\subsection{Returns}{
List of Well objects
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-WellHandle-store"></a>}}
\if{latex}{\out{\hypertarget{method-WellHandle-store}{}}}
\subsection{Method \code{store()}}{
Store Well objects in the database
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{WellHandle$store(well.list)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{well.list}}{A list of well objects}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-WellHandle-clone"></a>}}
\if{latex}{\out{\hypertarget{method-WellHandle-clone}{}}}
\subsection{Method \code{clone()}}{
The objects of this class are cloneable with this method.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{WellHandle$clone(deep = FALSE)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{deep}}{Whether to make a deep clone.}
}
\if{html}{\out{</div>}}
}
}
}