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

Description Usage Arguments Value

View source: R/celltype.R

Description

Contruct the knowledge base for cell type enrichment analysis

Usage

1
2
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


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