The "Single Cell Expression Set" (SCESet) class

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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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