# The "Single Cell Expression Set" (SCESet) class

### Description

S4 class and the main class used by scater to hold single cell expression data. SCESet extends the basic Bioconductor ExpressionSet class.

### Details

This class is initialized from a matrix of expression values.

Methods that operate on SCESet objects constitute the basic scater workflow.

### Slots

`logged`

:Scalar of class

`"logical"`

, indicating whether or not the expression data in the 'exprs' slot have been log2-transformed or not.`logExprsOffset`

:Scalar of class

`"numeric"`

, providing an offset applied to expression data in the 'exprs' slot when undergoing log2-transformation to avoid trying to take logs of zero.`lowerDetectionLimit`

:Scalar of class

`"numeric"`

, giving the lower limit for an expression value to be classified as "expressed".`cellPairwiseDistances`

:Matrix of class

`"numeric"`

, containing pairwise distances between cells.`featurePairwiseDistances`

:Matrix of class

`"numeric"`

, containing pairwise distances between features.`reducedDimension`

:Matrix of class

`"numeric"`

, containing reduced-dimension coordinates for cells (generated, for example, by PCA).`bootstraps`

:Array of class

`"numeric"`

that can contain bootstrap estimates of the expression or count values.`sc3`

:List containing results from consensus clustering from the SC3 package.

`featureControlInfo`

:Data frame of class

`"AnnotatedDataFrame"`

that can contain information/metadata about sets of control features defined for the`SCESet`

object. bootstrap estimates of the expression or count values.`useForExprs`

:Character string (one of 'exprs','tpm','counts' or 'fpkm') indicating which expression representation both internal methods and external packages should use. Defaults to 'exprs'.

### References

Thanks to the Monocle package (github.com/cole-trapnell-lab/monocle-release/) for their CellDataSet class, which provided the inspiration and template for SCESet.