BuildPriorInteraction: Build unweighted summarized interaction graph

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

Build unweighted summarized interaction graph

Description

Build unweighted summarized interaction graph

Usage

BuildPriorInteraction(
  object,
  assay = "SCT",
  slot = "data",
  species = "human",
  database = "OmniPath",
  ligands = NULL,
  recepts = NULL,
  specific = F,
  ranked_genes = NULL,
  correct.depth = T,
  graph_name = "prior_interaction"
)

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	Name of species for which to pull ligand-receptor interactions. One of "human", "mouse", or "rat"
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.
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
correct.depth	Correct summarized interaction graph for sequencing depth by linear regression. The sequencing depth of a cell-cell pair is the sum of UMI counts for each cell
graph_name	Name of summarized interaction graph to place into output. Default "prior_interaction"

Value

Returns a Seurat object with an unweighted summarized interaction graph in the Graphs slot

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