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>MAST:::Mandatory_Cellvars</code>
mapNames for the FluidigmAssay class are in the object <code>MAST:::FluidigmMapNames</code>

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

Greg Finak

MAST

Model-based Analysis of Single Cell Transcriptomics

SingleCellAssay-class function

SingleCellAssay extends class <code><a rd-options="" href="/link/DataLayer?package=MAST&version=0.931" data-mini-rdoc="MAST::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