FindIntegrationAnchors: Find integration anchors

In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

Description

Finds the integration anchors

Usage

FindIntegrationAnchors(object.list = NULL, assay = NULL,
  anchor.features = 2000, scale = TRUE, l2.norm = TRUE,
  dims = 1:30, k.anchor = 5, k.filter = 200, k.score = 30,
  max.features = 200, eps = 0, verbose = TRUE)

Arguments

object.list	A list of objects between which to find anchors for downstream integration.
assay	A vector of assay names specifying which assay to use when constructing anchors. If NULL, the current default assay for each object is used.
anchor.features	Can be either: A numeric value. This will call SelectIntegrationFeatures to select the provided number of features to be used in anchor finding A vector of features to be used as input to the anchor finding process
scale	Whether or not to scale the features provided. Only set to FALSE if you have previously scaled the features you want to use for each object in the object.list
l2.norm	Perform L2 normalization on the CCA cell embeddings after dimensional reduction
dims	Which dimensions to use from the CCA to specify the neighbor search space
k.anchor	How many neighbors (k) to use when picking anchors
k.filter	How many neighbors (k) to use when filtering anchors
k.score	How many neighbors (k) to use when scoring anchors
max.features	The maximum number of features to use when specifying the neighborhood search space in the anchor filtering
eps	Error bound on the neighbor finding algorithm (from RANN)
verbose	Print progress bars and output

Value

Returns an AnchorSet object

atakanekiz/Seurat3.0 documentation built on May 26, 2019, 2:33 a.m.