FindCircuits: Identify circuits between two timepoints

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

Identify circuits between two timepoints

Description

Identify circuits between two timepoints

Usage

FindCircuits(
  seu,
  nnr,
  ranked_genes,
  tps,
  split.by = "orig.ident",
  assay.use = "SCT",
  slot.use = "data",
  pearson.cutoff = 0.075
)

Arguments

seu	A binned Seurat object with binning results stored in the "bins" column of the meta.data slot
nnr	Ligand and target ranking results from NicheNet. Currently only the output of PrioritizeLigands is supported.
ranked_genes	Single-cell gene signatures, output from crGeneSig
tps	Character vector of two timepoints between which to find circuits. Time point identities must be in the correct sequential order.
split.by	Meta.data column name indicating how full dataset should be split. This corresponds to the column that contain time point information
assay.use	Name of assay from which to gather gene expression data
slot.use	Name of slot within assay from which to gather gene expression data
pearson.cutoff	numeric. Threshold for determining which ligand activities are "active". Ligands below this threshold will be considered inactive and not used for weighting. Default: 0.075

Value

Returns a data.frame containing all single-cell level circuits between two timepoints of a dataset

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