TransCommuProfile: get CommuProfile from a Cellwave objects

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

Description

get CommuProfile from a Cellwave objects

Usage

TransCommuProfile(
  object,
  pValueCor = 0.05,
  CorValue = 0.1,
  topTargetCor = 1,
  p.adjust = 0.05,
  use.type = "median",
  probs = 0.75,
  method = "weighted",
  Org = "Homo sapiens",
  IS_core = TRUE
)

Arguments

object	a Cellwave objects
pValueCor	firlter target gene of TF with spearson, p > pValueCor, default is 0.05
CorValue	firlter target gene of TF with spearson, value > CorValue, default is 0.1
topTargetCor	use topTargetCor of candidate genes which has firlter by above parameters, default is 1, means 100%
p.adjust	gsea pValue of regulons with BH adjusted threshold, default is 0.05
use.type	the type of compute, default is "median"
probs	Percentile of gene expression in one cell type to represents this cell type
method	"weighted", "max", "mean", of which "weighted" is default. choose the proper method to score downstream activation of ligand-receptor all regulons of given ligand-receptor relation
Org	choose the species source of gene, eg "Homo sapiens", "Mus musculus"
IS_core	logical variable ,whether use reference LR data or include extended datasets

Value

the value of cellwave object

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