CreateNichConObject: create a Cellwave objects

In ShellyCoder/cellcall: inference of intercellular networks from single-cell transcriptomics

create a Cellwave objects

Description

create a Cellwave objects

Usage

CreateNichConObject(
  data,
  min.feature = 3,
  names.field = 1,
  names.delim = "_",
  project = "Microenvironment",
  source = "UMI",
  scale.factor = 10^6,
  Org = "Homo sapiens"
)

Arguments

data	a dataframe with row of gene and column of sample
min.feature	Include cells where at least this many features are detected
names.field	BARCODE_CELLTYPE in the input matrix, set names.field to 2 to set the initial identities to CELLTYPE.
names.delim	For the initial identity class for each cell, choose this delimiter from the cell's column name. E.g. If your cells are named as BARCODE_CELLTYPE, set this to "_" to separate the cell name into its component parts for picking the relevant field.
project	Project name for the this object
source	the type of expression dataframe, eg "UMI", "fullLength", "TPM", or "CPM"
scale.factor	set the scale factor, default "10^6"
Org	choose the species source of gene, eg "Homo sapiens", "Mus musculus"

Value

the value of cellwave object

ShellyCoder/cellcall documentation built on Oct. 11, 2023, 2:50 p.m.