The StdAssay class is a virtual class that provides core
infrastructure for assay data in Seurat. Assays contain expression
data (layers) and associated feature-level meta data. Derived classes
(eg. the v5 Assay) may optionally
define additional functionality
layersA named list containing expression matrices; each matrix should
be a two-dimensional object containing some subset of cells and features
defined in the cells and features slots. Cell and feature
membership is recorded in the cells and features slots,
respectively
cellsA logical mapping of cell names and layer membership; this map contains all the possible cells that this assay can contain. New layers must have some subset of cells present in this map
featuresA logical mapping of feature names and layer membership; this map contains all the possible features that this assay can contain. New layers must have some subset of features present in this map
defaultA one-length integer with the end index of the
default layer; the default layer be
all layers up to and including the layer at index default
assay.origOriginal assay that this assay is based off of; used to track assay provenance
meta.dataA data frame with feature-level
meta data; should have the same number of rows as features
miscA named list of unstructured miscellaneous data
keyA one-length character vector with the object's key; keys must
be one or more alphanumeric characters followed by an underscore
“_” (regex pattern
“SeuratObject:::.KeyPattern()”)
Assay5-class Assay5T-class
v5 Standard Assay object, validity, and interaction methods
$.StdAssay(),
.DollarNames.StdAssay(),
StdAssay-validity,
[.StdAssay(),
[[.StdAssay(),
dim.StdAssay(),
dimnames.StdAssay(),
show,StdAssay-method,
split.StdAssay(),
subset.StdAssay()