celltype.enrichment: Perform cell type enrichment

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

Description

Perform cell type enrichment

Usage

celltype.enrichment(object, species = "MUSMU", id.type = "SYMBOL",
  do.plot = T, top.k = 5, verbose = T, ...)

Arguments

object	A sincera oject
species	The species of the data, possible values include MUSMU - mouse, HOMSA - human
id.type	The type of gene identifier, possible values include SYMBOL - Entrez SYMBOL, EG - Entrez ID, ENSEMBL - Ensembl ID
do.plot	If TRUE, plot top enriched cell types per group at the end of the analysis
top.k	The number of top enriched cell types to be plotted at the end of the analysis
verbose	If TRUE, print verbose messages

Details

Please note that the default gene-celltype association table was constructed based on mouse genes. The use of this function for human single cell analysis is still under testing.

Value

The updated sincera object with enrichment results in the cte slot

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