celltalk: Assess ligand and receptor interactions across groups of...

In arc85/celltalker: Analysis of cell-cell communication from single-cell RNAseq data

Assess ligand and receptor interactions across groups of cells

Description

Assess ligand and receptor interactions across groups of cells

Usage

celltalk(
  input_object,
  metadata_grouping = cell_types,
  ligand_receptor_pairs = ramilowski_pairs,
  number_cells_required = 100,
  min_expression = 1000,
  max_expression = 20000,
  scramble_times = 10
)

Arguments

input_object	Seurat object to create ligand receptor matrices from
metadata_grouping	Grouping variable in the Seurat object metadata used to define the groups of cells. Default is "cell_types".
ligand_receptor_pairs	Data.frame of ligands, receptors and interactions in the format of ramilowski_pairs provided by this package. Defaults is "ramilowski_pairs".
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

Comprehensive tibble of cognate ligand and receptor interactions and statistical significance of these interactions across cell types.

arc85/celltalker documentation built on July 2, 2023, 2:07 p.m.