AlignDatasets: Align Datasets through binning

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

Align Datasets through binning

Description

Align Datasets through binning

Usage

AlignDatasets(
  seuObj,
  split.by = "time.orig",
  dims = 1:50,
  snn.reduction = "pca",
  anchor_score_threshold = 0.5,
  optim_quan.threshold = 0.1,
  optim_k.unique = 6,
  verbose = F
)

Arguments

seuObj	A seurat object
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
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

Value

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

Examples

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

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