ConnectProfile: 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

ConnectProfile(
  object,
  pValueCor = 0.05,
  CorValue = 0.1,
  topTargetCor = 1,
  method = "weighted",
  p.adjust = 0.05,
  use.type = "median",
  probs = 0.9,
  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%
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
p.adjust	gsea pValue of regulons with BH adjusted threshold, default is 0.05
use.type	With parameter "median", CellCall set the mean value of gene as zero, when the percentile of gene expression in one celltype below the parameter "probs". The other choice is "mean" and means that we not concern about the percentile of gene expression in one celltype but directly use the mean value.
probs	Set the percentile of gene expression in one celltype to represent mean value, when use.type="median".
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 result dataframe of cell communication

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