CreateObject_fromSeurat: Create Nichobject from Seurat object

In shouguog/cellcallEXT: inference of intercellular networks from single-cell transcriptomics

Description

Create Nichobject from Seurat object

Usage

CreateObject_fromSeurat(
  Seurat.object,
  slot = "counts",
  status = NULL,
  expDirection = "BOTH",
  cell_type = "orig.ident",
  data_source = "UMI",
  scale.factor = 10^6,
  Org = "Homo sapiens"
)

Arguments

Seurat.object	The Seurat object which stores the expression matrix and cell type information
slot	The name of slot which contains expression matrix, default "counts".
status	the status of cell disease or control
expDirection	the direction of expression change UP DOWN or BOTH
cell_type	The name of specific column which contains cell type information, default "orig.ident".
scale.factor	set the scale factor, default "10^6"
Org	the species of this scRNA-seq
source	the type of expression dataframe, eg "UMI", "fullLength", "TPM", or "CPM"

shouguog/cellcallEXT documentation built on Jan. 2, 2022, 8:13 p.m.