Run Seurat MapQuery to reference

This will find transfer anchors between query and reference, and map the query to the reference. For SCT-normalized references, Seurat::FindTransferAnchors() handles query normalization internally by recomputing residuals using the reference's SCT model (recompute.residuals = TRUE by default), so a manual call to Seurat::SCTransform() on the query is NOT needed. For LogNormalize references, the query is normalized with Seurat::NormalizeData() prior to anchor finding.

Usage

RunSeuratMap2Ref(
  object,
  ref,
  use,
  ident = "seurat_clusters",
  refnorm = c("auto", "LogNormalize", "SCT", "SCTransform"),
  skip_if_normalized = TRUE,
  split_by = NULL,
  ncores = 1,
  MapQueryArgs = list(refdata = list()),
  FindTransferAnchorsArgs = list(),
  SCTransformArgs = list(),
  NormalizeDataArgs = list(),
  log = NULL,
  cache = NULL
)

Arguments

object

Seurat object

ref

Reference Seurat object or a file path to a Seurat object with .rds or .h5seurat extension

use

The name in the metadata of the reference to use as identity for the query after mapping

ident

The name of the identity in metadata after mapping

refnorm

The normalization method used by the reference. The same normalization method will be used for the query.

"auto": automatically detect the normalization method used by the reference
"LogNormalize": LogNormalize
"SCT": SCTransform
"SCTransform": SCTransform (alias for SCT)

skip_if_normalized

For LogNormalize, skip Seurat::NormalizeData() if the query's default assay is already 'RNA' (i.e., already log-normalized). For SCT with FindTransferAnchorsArgs$recompute.residuals = FALSE, skip Seurat::SCTransform() if the default assay is already 'SCT'. This parameter has no effect in the default SCT case (recompute.residuals = TRUE), where Seurat::FindTransferAnchors() handles normalization internally using the reference model.

split_by

The name of the metadata to split the query object by and do the mapping separately

ncores

Number of cores to use for parallel processing for the split query objects

MapQueryArgs

Arguments to pass to Seurat::MapQuery(). The use argument will be added to the refdata list.

FindTransferAnchorsArgs

Arguments to pass to Seurat::FindTransferAnchors().

SCTransformArgs

Arguments to pass to Seurat::SCTransform(). Only used when refnorm is set to "SCT" AND FindTransferAnchorsArgs$recompute.residuals is explicitly set to FALSE. In the default case (recompute.residuals = TRUE), Seurat::FindTransferAnchors() recomputes query residuals from raw counts using the reference SCT model, making manual Seurat::SCTransform() on the query unnecessary.

NormalizeDataArgs

Arguments to pass to Seurat::NormalizeData(). Will be used to normalize the query object if refnorm is set to "LogNormalize"

log

Logger

cache

Directory to cache the results. Set to FALSE to disable caching

Value

The Seurat object with the mapped data

Usage

Arguments

Value

See also