celltype.enrichment.initKB: Contruct the knowledge base for cell type enrichment analysis

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

Description

Contruct the knowledge base for cell type enrichment analysis

Usage

celltype.enrichment.initKB(associations, genome, species = "MUSMU",
  id.type = "ENSEMBL", verbose = T)

Arguments

associations	(data.frame) a data frame containing the gene and cell type associations
genome	(character) the full set of genes in a scRNA-seq data
species	(character) the species of the genome: MUSMU - mouse, HOMSA - human
id.type	(character) the type of ids of the genes in the genome: ENSEMBL - ENSEMBL gene id, SYMBOL - Entrez Gene Symbol, EG - Entrez Gene Id
verbose	(logical)

Value

a list of 3 items: celltype.gene.association - genome related associations, celltype.genome.count - genome-wide cell type associations, genome - symbol mapping for the genome

minzheguo/SINCERA documentation built on Feb. 3, 2021, 2:31 p.m.