analyzeGOSeurat {scGOclust}

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,
  ...
)

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

Value

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")