getCellTypeSharedGO function

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

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)

Returns

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)