MapTo: Map query Seurat object to reference Seurat object

In BruceRheaume/CellTools: What the Package Does (One Line, Title Case)

Map query Seurat object to reference Seurat object

Description

This function is a wrapper for Seurat's TransferData, IntegrateEmbeddings, and ProjectUMAP functions, meant to be run after OptiK, as part of the Denoise/OptiK/MapTo pipeline.

Usage

MapTo(
  ref,
  query,
  lab = "seurat_clusters",
  k = "opti",
  get.anchors = T,
  dims = 30
)

Arguments

ref	Reference Seurat object
query	Wuery Seurat object
lab	The reference label to treat as clusters. Default is "seurat_clusters"
k	The k-weight to use when weighting anchors. Default is opti
get.anchors	A logical that when true will first run Seurat's FindTransferAnchors. Default is TRUE.
dims	Number of PCs to use when get.anchors = T. Default is 30

Value

Returns a Seurat object with a new slot where the k-weight is stored: misc$CellTools$opti_k

References

Rheaume, B. A., & Trakhtenberg, E. F. (2022). Self-learning algorithm for denoising and advancing the integration of scRNA-seq datasets improves the identification of resilient and susceptible retinal ganglion cell types bioRxiv.

BruceRheaume/CellTools documentation built on April 24, 2022, 7:03 p.m.