SingleCellAssay-class

SingleCellAssay represents an arbitrary single cell assay
It is meant to be flexible and is subclassed to represent
specific assay types like Fluidigm and NanoString. It
should be constructed using the <code>SingleCellAssay</code>,
<code>SCASet</code> or subclass constructors. mapNames for the
SingleCellAssay class are in the object
<code>SingleCellAssay:::Mandatory_Cellvars</code> mapNames for
the FluidigmAssay class are in the object
<code>SingleCellAssay:::FluidigmMapNames</code>

Core data structures and methods for handling single cell assay
data.

Greg Finak

SingleCellAssay

Core data structures for single-cell assays

SingleCellAssay-class function

SingleCellAssay extends class
<code><a rd-options="" href="/link/DataLayer?package=SingleCellAssay&version=0.80" data-mini-rdoc="SingleCellAssay::DataLayer">DataLayer</a></code>, so inherits its slots and methods.
It also contains the following additional slots:<dl class="dl-horizontal">
<dt>featureData</dt><dd>an <code>AnnotatedDataFrame</code> that
describes feature-level metadata (i.e. genes)</dd>
<dt>phenoData</dt><dd>an <code>AnnotatedDataFrame</code> that
describes the phenotype-level metadata (i.e. subject or
experimental unit)</dd> (not yet implemented)
<dt>cellData</dt><dd>an <code>AnnotatedDataFrame</code> that describes
the cell-level metadata (i.e. per individual cell)</dd>
<dt>description</dt><dd>a <code>data.frame</code></dd> <dt>id</dt><dd>a vector
of type <code>character</code> that identifies the set of columns
acting as a primary key to uniquely identify a single-cell
or single-well across all wells / cells / assays / subjects
/ conditions in the data set.</dd> </dl>

Slots

SingleCellAssay class — SingleCellAssay-class

SingleCellAssay extends class
<code><a rd-options='' href='DataLayer'>DataLayer</a></code>, so inherits its slots and methods.
It also contains the following additional slots:<dl class='dl-horizontal'>
<dt>featureData</dt><dd>an <code>AnnotatedDataFrame</code> that
describes feature-level metadata (i.e. genes)</dd>
<dt>phenoData</dt><dd>an <code>AnnotatedDataFrame</code> that
describes the phenotype-level metadata (i.e. subject or
experimental unit)</dd> (not yet implemented)
<dt>cellData</dt><dd>an <code>AnnotatedDataFrame</code> that describes
the cell-level metadata (i.e. per individual cell)</dd>
<dt>description</dt><dd>a <code>data.frame</code></dd> <dt>id</dt><dd>a vector
of type <code>character</code> that identifies the set of columns
acting as a primary key to uniquely identify a single-cell
or single-well across all wells / cells / assays / subjects
/ conditions in the data set.</dd> </dl>

SingleCellAssay-class: SingleCellAssay class

Description

Arguments

Slots

See Also