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.


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