InterCom: Reconstructs functional cell-cell communication networks

In saschajung/Intercom: Reconstruction of Functional Cell-Cell Communication Networks

Reconstructs functional cell-cell communication networks

Description

Reconstructs functional cell-cell communication networks for a given dataset.

Usage

InterCom(
  data,
  anno.tbl,
  species,
  sighot.cutoff = 0.1,
  sighot.percentile = 70,
  consv.thrs = 0.05,
  ncores = 4,
  sig.cutoff = 0.9,
  z.score.cutoff = 2,
  min.cells = 10,
  tissue.name,
  temp.folder.name = "temp",
  out.path
)

Arguments

data	Matrix or data frame of expression values; rows have to correspond to genes and columns to cells. Row names must be gene symbols while column names can be any identifier for a cell. Raw counts or normalized data is permitted.
anno.tbl	Data frame annotating each cell with a cluster/cell type. Cell names have to be provided in the first and cluster/cell type information in the second column.
species	The organism from which the data was obtained. Currently, only "MOUSE" and "HUMAN" are supported
sighot.cutoff	Cutoff parameter for SigHotSpotter. Can be between 0 and 1.
sighot.percentile	Percentile parameter for SigHotSpotter. Can be between 0 and 100.
consv.thrs	Fraction of cells per cluster/cell type that must express a ligand, receptor or TF to be considered.
ncores	Number of cores to use. Depending on the machine, can be any integer value greater or equal to 1.
sig.cutoff	Significance cutoff between 0 (weakest) and 1 (strictest). Default: 0.9
z.score.cutoff	Cutoff parameter to determine significant associations between receptors and interface TFs. Default: 2.
min.cells	The minimum number of cells/samples per cell type. Default: 10
tissue.name	A name of the dataset
temp.folder.name	Name of the temporary folder to be created within the output path. Default: "temp"
out.path	Path to a folder where the output should be stored.

Value

List object containing the final interactome and auxiliary information

saschajung/Intercom documentation built on May 27, 2023, 5:11 p.m.