slice: The slice Class

In minzheguo/SLICE: Determining Cell Differentiation and Lineage based on Single Cell Entropy

The slice Class

Description

The object storing all information associated with the slice analysis, including data, annotations, analyes, etc.

Details

Information is stored in slots. Key slots include:

Slots

data:

"ExpressionSet", the scRNA-seq data in ExpressionSet format, encoding the expression matrix, and cell and gene information

ident:

"vector", the identity (cluster/state/type) of cells

ident.slice:

"vector", the identity (cluster/state/type) of single cells inferred by SLICE

ident.original:

"vector", the original identity (cluster/state/type) of single cells provided by the user during object construction

entropy:

"vector", the entropy of single cells

vds:

"data.frame", a data frame containing the x and y coordinates of cells for visualization

rds:

"data.frame", a data frame containing reduced dimensions of each cell

model:

"list", a list containing slice inferred lineage model

transitions:

"list", a list containing slice inferred cell trajectories

profiles:

"list", a list containing slice inferred cell trajectory dependent gene expression profiles

projname:

"character", a string describing the analysis

minzheguo/SLICE documentation built on June 5, 2023, 11:56 a.m.