IntegrateData: Integrate data

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

Description

Integrates the data

Usage

IntegrateData(anchorset, new.assay.name = "integrated",
  features = NULL, features.to.integrate = NULL, dims = 1:30,
  k.weight = 100, sd.weight = 1, sample.tree = NULL,
  preserve.order = FALSE, do.cpp = TRUE, eps = 0, verbose = TRUE)

Arguments

anchorset	Results from FindIntegrationAnchors
new.assay.name	Name for the new assay containing the integrated data
features	Vector of features to use when computing the PCA to determine the weights. Only set if you want a different set from those used in the anchor finding process
features.to.integrate	Vector of features to integrate. By default, will use the features used in anchor finding.
dims	Number of PCs to use in the weighting procedure
k.weight	Number of neighbors to consider when weighting
sd.weight	Controls the bandwidth of the Gaussian kernel for weighting
sample.tree	Specify the order of integration. If null, will compute automatically.
preserve.order	Integrate the objects in the order they were provided to FindAnchors
do.cpp	Run cpp code where applicable
eps	Error bound on the neighbor finding algorithm (from RANN)
verbose	Print progress bars and output

Value

Returns a Seurat object with a new integrated Assay

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