cellTypeGOCorr: calculate correlation between cell types represented by...

In scGOclust: Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq

calculate correlation between cell types represented by scaled GO, per-species

Description

calculate correlation between cell types represented by scaled GO, per-species

Usage

cellTypeGOCorr(cell_type_go, corr_method = "pearson")

Arguments

cell_type_go	cell type GO table calculated via getCellTypeGO
corr_method	correlation method, choose among "pearson", "kendall", "spearman", default 'pearson'

Value

a dataframe with correlation between cell types

Examples

library(scGOclust)
library(httr)
httr::set_config(httr::config(ssl_verifypeer = FALSE))
data(mmu_tbl)
data(mmu_subset)
go_seurat_obj = makeGOSeurat(ensembl_to_GO = mmu_tbl,
 seurat_obj = mmu_subset,
 feature_type = "external_gene_name")

cell_type_go = getCellTypeGO(go_seurat_obj = go_seurat_obj, cell_type_co = "cell_type_annotation")

cellTypeGOCorr(cell_type_go = cell_type_go, corr_method = "pearson")

scGOclust documentation built on May 29, 2024, 8:59 a.m.