FindAllCircuits: Find all circuits in a multi-timepoint longitudinal dataset

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

Find all circuits in a multi-timepoint longitudinal dataset

Description

Find all circuits in a multi-timepoint longitudinal dataset

Usage

FindAllCircuits(
  seu,
  nnr,
  ranked_genes = NULL,
  all.tps = NULL,
  subsample = F,
  subsample.n = 1e+05
)

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
all.tps	Character vector of all timepoints between which to find circuits. Time point identities must be in the correct sequential order.
subsample	logical. Subsample circuits for each pair of timepoints to the threshold set in subsample.n?
subsample.n	numeric. If subsample=T, subsample circuits from each timepoint pair to this level

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