Finds the integration anchors
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)A list of objects between which to find anchors for downstream integration.
A vector of assay names specifying which assay to use when constructing anchors. If NULL, the current default assay for each object is used.
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
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
Perform L2 normalization on the CCA cell embeddings after dimensional reduction
Which dimensions to use from the CCA to specify the neighbor search space
How many neighbors (k) to use when picking anchors
How many neighbors (k) to use when filtering anchors
How many neighbors (k) to use when scoring anchors
The maximum number of features to use when specifying the neighborhood search space in the anchor filtering
Error bound on the neighbor finding algorithm (from RANN)
Print progress bars and output
Returns an AnchorSet object