The Seurat object is a representation of single-cell expression data for R;
each Seurat object revolves around a set of cells and consists of one or more
Assay
objects, or individual representations of
expression data (eg. RNA-seq, ATAC-seq, etc). These assays can be reduced
from their high-dimensional state to a lower-dimension state and stored as
DimReduc
objects. Seurat objects also
store additional metadata, both at the cell and feature level (contained
within individual assays). The object was designed to be as self-contained as
possible, and easily extendable to new methods.
assays
A list of assays for this project
meta.data
Contains meta-information about each cell, starting with
number of features detected (nFeature) and the original identity class
(orig.ident); more information is added using AddMetaData
active.assay
Name of the active, or default, assay; settable using
DefaultAssay
active.ident
The active cluster identity for this Seurat object;
settable using Idents
graphs
A list of Graph
objects
neighbors
...
reductions
A list of dimensional reduction objects for this object
images
A list of spatial image objects
project.name
Name of the project
misc
A list of miscellaneous information
version
Version of Seurat this object was built under
commands
A list of logged commands run on this Seurat
object
tools
A list of miscellaneous data generated by other tools, should be
filled by developers only using Tool<-
Seurat object, validity, and interaction methods
$.Seurat()
,
Seurat-validity
,
[[.Seurat()
,
[[<-,Seurat
,
[[<-,Seurat,NULL
,
dim.Seurat()
,
dimnames.Seurat()
,
merge.Seurat()
,
names.Seurat()
,
subset.Seurat()