SCESet {scater} | R Documentation

## 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

`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.

### 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.

[Package scater version 1.6.3 Index]