scGOclust (version 0.2.1)

getCellTypeSharedGO: 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
)

Value

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

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)

Examples

# \donttest{
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)
# }