FastRPCAIntegration: Perform integration on the joint PCA cell embeddings.
In satijalab/seurat: Tools for Single Cell Genomics

FastRPCAIntegration

R Documentation

Perform integration on the joint PCA cell embeddings.

Description

This is a convenience wrapper function around the following three functions that are often run together when perform integration. #' FindIntegrationAnchors, RunPCA, IntegrateEmbeddings.

Usage

FastRPCAIntegration(
  object.list,
  reference = NULL,
  anchor.features = 2000,
  k.anchor = 20,
  dims = 1:30,
  scale = TRUE,
  normalization.method = c("LogNormalize", "SCT"),
  new.reduction.name = "integrated_dr",
  npcs = 50,
  findintegrationanchors.args = list(),
  verbose = TRUE
)

Arguments

`object.list`	A list of `Seurat` objects between which to find anchors for downstream integration.
`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.
`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
`k.anchor`	How many neighbors (k) to use when picking anchors
`dims`	Which dimensions to use from the CCA to specify the neighbor search space
`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
`normalization.method`	Name of normalization method used: LogNormalize or SCT
`new.reduction.name`	Name of integrated dimensional reduction
`npcs`	Total Number of PCs to compute and store (50 by default)
`findintegrationanchors.args`	A named list of additional arguments to `FindIntegrationAnchors`
`verbose`	Print messages and progress