getCellTypeSharedGO: get shared up and down regulated GO terms for all pairs of...

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

get shared up and down regulated GO terms for all pairs of cell types

Description

get shared up and down regulated GO terms for all pairs of cell types

Usage

getCellTypeSharedGO(
  species_1,
  species_2,
  analyzed_go_seurat_sp1,
  analyzed_go_seurat_sp2,
  cell_type_col_sp1,
  cell_type_col_sp2,
  layer_use = "data",
  p_val_threshould = 0.01
)

Arguments

species_1	name of species one
species_2	name of species two
analyzed_go_seurat_sp1	analyzed GO seurat object of species one
analyzed_go_seurat_sp2	analyzed GO seurat object of species two
cell_type_col_sp1	cell type column name for species 1 data
cell_type_col_sp2	cell type column name for species 2 data
layer_use	layer to use for marker computation, default 'data' which after NormalizeData will be log1p normalized data.
p_val_threshould	p value threshold for selecting DEG (p_adjust)

Value

a list with sp1 raw, sp2 raw and shared, significant up and down regulated GO terms per cell type (pair)

Examples

library(scGOclust)
library(httr)
httr::set_config(httr::config(ssl_verifypeer = FALSE))
data(mmu_tbl)
data(mmu_subset)
data(dme_tbl)
data(dme_subset)

mmu_go_obj = makeGOSeurat(ensembl_to_GO = mmu_tbl,
 seurat_obj = mmu_subset,
 feature_type = "external_gene_name")
dme_go_obj = makeGOSeurat(ensembl_to_GO = dme_tbl,
 seurat_obj = dme_subset,
 feature_type = "external_gene_name")


mmu_go_obj_analyzed = analyzeGOSeurat(mmu_go_obj, "cell_type_annotation")
dme_go_obj_analyzed = analyzeGOSeurat(dme_go_obj, "annotation")

getCellTypeSharedGO(species_1 = 'mmusculus',
species_2 = 'dmelanogaster',
analyzed_go_seurat_sp1 =  mmu_go_obj_analyzed,
analyzed_go_seurat_sp2 =  dme_go_obj_analyzed,
cell_type_col_sp1 = 'cell_type_annotation',
cell_type_col_sp2 = 'annotation',
layer_use = "data",
p_val_threshould = 0.01)

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