sincera: The sincera Class

In xu-lab/SINCERA: An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

Description

The object storing all information associated with the sincera analysis, including data, annotations, analyes, etc. It is recommended to use the defined get and set methods to access and manipulate the data in the sincera object.

Details

Information is stored in slots. Key slots include:

Slots

data:

"ExpressionSet", the scRNA-seq data in ExpressionSet format, encoding the expression matrix, gene, and cell metadata, including sample and condition information. In most of the SINCERA functions, cell grouping is based on the "GROUP" metadata.

genes.forclustering:

"vector", the set of genes used for the cell cluster identification

difftests:

"list", results of differential expression test of all genes in the data using different methods

siggenes:

"data.frame", a data frame containing the significant differentially expressed genes

cte:

"list", results of cell type enrichment

ctmap:

"data.frame", a data frame containing the mapping between cell clusters and cell types

markers:

"data.frame", a data frame containing known cell type markers

siggenes:

"data.frame", a data frame containing the signature genes based on signature prediction

sigvalidate:

"data.frame", a data frame containing the results of signature validation

df:

"list", a list containing the results of driving force analysis

associations:

"data.frame", a data frame containing the gene and cell type association table

tfs:

"vector", a vector containing a set of all transcription factors/cofactors

projname:

"character", a string describing the data and analysis

xu-lab/SINCERA documentation built on Feb. 3, 2021, 4:19 a.m.