perform.celltalker: Infers cell-to-cell communications.

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Infers cell-to-cell communications.

Description

Find ligand-receptor communcations between cell types.

Usage

add.cell.cycle(object = obj, assay = 'RAW', slot = 'counts')

Arguments

object	IBRAP S4 class object
assay	A character string containing indicating which assay to use
slot	String. indicating which slot within the assay should be sourced
clust.method	String. can be either metadata or a dataframe stored in cluster_assignments
column	String. name of the column to access in the clust.method
number_cells_required	Number of cells per group required to perform analysis of ligand/receptor interactions. Defaults to 100.
min_expression	Minimum expression in counts to consider a ligand or receptor for interactions analysis. A sensible default is set to 1000, but is dataset dependent. This is meant to filter out lowly expressed ligands and receptors.
max_expression	Maxmium expression in counts to consider a ligand or receptor for interactions analysis. A sensible default is set to 20000, but is dataset dependent. This is meant to filter out ubiquitously expressed ligands and receptors.
scramble_times	Number of times to scamble ligand/receptor interactions to create a background distribution for statistical comparison.

Value

dataframe of inferred cell-to-cell communications

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.