IntegrateData.STACAS: IntegrateData.STACAS

In carmonalab/STACAS: STACAS: Sub-Type Anchoring Correction for Alignment in Seurat

IntegrateData.STACAS

Description

Integrate a list of datasets using STACAS anchors. Based on the IntegrateData function from Seurat. This function requires that you have calculated a set of integration anchors using FindAnchors.STACAS. To perform semi-supervised integration, run FindAnchors.STACAS with cell type annotations labels. Integration anchors with inconsistent cell type will be excluded from integration, providing an integrated space that is partially guided by prior information.

Usage

IntegrateData.STACAS(
  anchorset,
  new.assay.name = "integrated",
  features.to.integrate = NULL,
  dims = 30,
  k.weight = 100,
  sample.tree = NULL,
  hclust.method = c("single", "complete", "ward.D2", "average"),
  semisupervised = TRUE,
  verbose = TRUE
)

Arguments

anchorset	A set of anchors calculated using FindAnchors.STACAS
new.assay.name	Assay to store the integrated data
features.to.integrate	Which genes to include in the corrected integrated space (def. variable genes)
dims	Number of dimensions for local anchor weighting
k.weight	Number of neighbors for local anchor weighting. Set k.weight="max" to disable local weighting
sample.tree	Specify the order of integration. See SampleTree.STACAS to calculate an integration tree.
hclust.method	Clustering method for integration tree (single, complete, average, ward)
semisupervised	Whether to use cell type label information (if available)
verbose	Print progress bar and output

Value

Returns a Seurat object with a new integrated Assay, with batch-corrected expression values

carmonalab/STACAS documentation built on Feb. 3, 2024, 7:42 a.m.