TransferSketchLabels: Transfer data from sketch data to full data

In Seurat: Tools for Single Cell Genomics

Transfer data from sketch data to full data

Description

This function transfers cell type labels from a sketched dataset to a full dataset based on the similarities in the lower dimensional space.

Usage

TransferSketchLabels(
  object,
  sketched.assay = "sketch",
  reduction,
  dims,
  refdata = NULL,
  k = 50,
  reduction.model = NULL,
  neighbors = NULL,
  recompute.neighbors = FALSE,
  recompute.weights = FALSE,
  verbose = TRUE
)

Arguments

object	A Seurat object.
sketched.assay	Sketched assay name. Default is 'sketch'.
reduction	Dimensional reduction name to use for label transfer.
dims	An integer vector indicating which dimensions to use for label transfer.
refdata	A list of character strings indicating the metadata columns containing labels to transfer. Default is NULL. Similar to refdata in 'MapQuery'
k	Number of neighbors to use for label transfer. Default is 50.
reduction.model	Dimensional reduction model to use for label transfer. Default is NULL.
neighbors	An object storing the neighbors found during the sketching process. Default is NULL.
recompute.neighbors	Whether to recompute the neighbors for label transfer. Default is FALSE.
recompute.weights	Whether to recompute the weights for label transfer. Default is FALSE.
verbose	Print progress and diagnostic messages

Value

A Seurat object with transferred labels stored in the metadata. If a UMAP model is provided, the full data are also projected onto the UMAP space, with the results stored in a new reduction, full.'reduction.model'

Seurat documentation built on May 29, 2024, 4:20 a.m.