BinDatasets: Align Datasets through binning

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

Align Datasets through binning

Description

Align Datasets through binning

Usage

BinDatasets(
  seu,
  split.by = "time.orig",
  dims = 1:50,
  coarse_cell_types = NULL,
  sigtest_cell_types = NULL,
  snn.reduction = "pca",
  anchor_score_threshold = 0.5,
  optim_quan.threshold = 0.1,
  optim_k.unique = NULL,
  verbose = F
)

Arguments

split.by	Name of meta.data column containing the factor by which the dataset will be split
dims	Dimensions of reduction to use as input for neighbor graph calculation
coarse_cell_types	Name of meta.data column containing cell type calls for binning. Each set of cell type calls will be binned separately.
sigtest_cell_types	Name of meta.data column containing the cell type labels to use for connectivity testing
snn.reduction	Name of reduction used as input to building the SNN
anchor_score_threshold	Anchor pairs scoring below this threshold will be discarded.
optim_quan.threshold	Percentage of poor connectivity bins to remove on each iteration of connectivity optimization
optim_k.unique	Mean number of datasets represented in each bin at which connectivity optimization will be considered complete
seuObj	A seurat object

Value

A binned Seurat object with bin assignments in the "bins" column of the meta.data slot

Examples

seu <- BinDatasets(seu, split.by = "time")

BlishLab/scriabin documentation built on July 5, 2023, 1:14 a.m.