integration_anchorset: Get integration anchorset from Seurat objects.

In altairwei/rhapsodykit: A Set of Tools for BD Rhapsody WTA Downstream Analysis

Get integration anchorset from Seurat objects.

Description

Get integration anchorset from Seurat objects.

Usage

integration_anchorset(
  obj_list,
  n_dims = 20,
  reduction = c("cca", "rpca"),
  k.anchor = 5,
  reference = NULL,
  normalization = "LogNormalize",
  verbose = TRUE,
  ...
)

Arguments

obj_list	A list of Seurat objects.
n_dims	Number of dimensions to use as input.
reduction	Dimensional reduction to perform when finding anchors. Can be one of: cca: Canonical correlation analysis rpca: Reciprocal PCA rlsi: Reciprocal LSI
k.anchor	How many neighbors (k) to use when picking anchors
reference	A vector specifying the object/s to be used as a reference during integration. If NULL (default), all pairwise anchors are found (no reference/s). If not NULL, the corresponding objects in object.list will be used as references. When using a set of specified references, anchors are first found between each query and each reference. The references are then integrated through pairwise integration. Each query is then mapped to the integrated reference.
normalization	Normalization method.
verbose	Print output
...	pass to FindIntegrationAnchors

Value

Returns an AnchorSet object that can be used as input to IntegrateData.

altairwei/rhapsodykit documentation built on Feb. 1, 2023, 8:52 a.m.