scGOclust (version 0.2.1)

analyzeGOSeurat: standard seurat analysis on GO_seurat object

Description

standard seurat analysis on GO_seurat object

Usage

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

Value

standard analyzed GO seurat object until UMAP

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

Examples

# \donttest{
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")
# }