analyzeGOSeurat function

standard seurat analysis on GO_seurat object

analyzeGOSeurat(
  go_seurat_obj,
  cell_type_col,
  norm_log1p = TRUE,
  scale.factor = 10000,
  nfeatures = 2000,
  cluster_res = 1,
  min.dist = 0.3,
  ...
)

Arguments

• go_seurat_obj: go seurat object created by makeGOSeurat
• cell_type_col: column name in mera.data storing cell type classes
• norm_log1p: whether or not to perform data normalisation and log1p transformation, default TRUE
• scale.factor: param for Seurat NormalizeData
• nfeatures: param for Seurat FindVariableFeatures
• cluster_res: resolution for Seurat FindClusters
• min.dist: param for Seurat RunUMAP
• ...: additional params for all Seurat functions involved in this function

Returns

standard analyzed GO seurat object until UMAP

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")

analyzeGOSeurat(go_seurat_obj = go_seurat_obj, cell_type_col = "cell_type_annotation")