InteractionPrograms: Discover co-expressed ligand-receptor interaction programs

In BlishLab/scriabin: Single-cell resolved interaction analysis through binning

Discover co-expressed ligand-receptor interaction programs

Description

Discover co-expressed ligand-receptor interaction programs

Usage

InteractionPrograms(
  object,
  assay = "SCT",
  slot = "data",
  species = "human",
  database = "OmniPath",
  ligands = NULL,
  recepts = NULL,
  iterate.threshold = 300,
  n.iterate = NULL,
  specific = F,
  ranked_genes = NULL,
  return.mat = T,
  softPower = NULL,
  r2_cutoff = 0.6,
  min.size = 5,
  plot.mods = F,
  tree.cut.quantile = 0.4,
  threads = NULL,
  cell_types = NULL,
  min.cell = 3,
  seed = 1111
)

Arguments

object	A seurat object
assay	Assay in Seurat object from which to pull expression values
slot	Slot within assay from which to pull expression values
species	character. Name of species from which to load ligand-receptor databases. One of: "human", "mouse", "rat". Default: "human"
database	Name of ligand-receptor database to use. Default: "OmniPath" When species is "human", one of: OmniPath, CellChatDB, CellPhoneDB, Ramilowski2015, Baccin2019, LRdb, Kirouac2010, ICELLNET, iTALK, EMBRACE, HPMR, Guide2Pharma, connectomeDB2020, talklr, CellTalkDB When species is "mouse" or "rat", only "OmniPath" is supported. To pass a custom ligand-receptor database to this function, set database = "custom"
ligands	Character vector of custom ligands to use for interaction graph generation. Ignored unless database = "custom" When ligands is supplied, recepts must also be supplied and equidimensional.
recepts	Character vector of custom receptors to use for interaction graph generation. Ignored unless database = "custom" When recepts is supplied, ligands must also be supplied and equidimensional.
iterate.threshold	When a dataset has more cells than iterate.threshold, the TOM will be approximated iteratively. For each iteration, a randomly subsampled dataset of size iterate.threshold will be used to construct the CCIM and generate the TOM.
n.iterate	For datasets larger than iterate.threshold, determines how many iterations to perform to approximate the TOM.
specific	logical. When TRUE, consider only the genes in each cell's predefined gene signature (see crGeneSig) as expressed. Default FALSE
ranked_genes	Cell-resolved gene signatures, used only when specific = T
return.mat	logical. Returns ligand-receptor covariance matrix and TOM along with modules and intramodular connectivity. Required for significance testing.
softPower	softPower threshold for adjacency matrix. If unspecified, will be chosen automatically based on the minimum softPower that results in a scale-free topology fitting index (R^2) of greater than r2_cutoff (by default 0.6)
r2_cutoff	The softPower will be chosen as the minimum value that satisfies a scale-free topology fitting index (R^2) of r2_cutoff (by default: 0.6)
min.size	Minimum size of each interaction program
plot.mods	Plot modules and associated dendrograms during analysis
tree.cut.quantile	The dendrogram tree height quantile at which the dendrogram should be cut. Higher values lead to fewer, smaller modules.
threads	To enable WGCNA multi-threading, specify the number of threads to allow. This parameter may be required when running on multiple cores
cell_types	meta.data column name corresponding to cell types or clusters. If iteratively approximating the TOM, when specified the sequences of subsampled CCIM will be sampled proportionally to annotations present in this grouping.
min.cell	When cell_types is specified, the minimum number of cells in a cell type that will be included when generating each iterative CCIM (default: 3)
seed	Seed (default: 1111)

Value

When return.mat = T, returns a list of length 4 containing ligand-receptor covariance matrix, TOM, module lists, and intramodular connectivity. Otherwise, returns a list of length 2 containing only module lists and intramodular connectivity.

BlishLab/scriabin documentation built on Sept. 16, 2024, 1:19 a.m.