ProjectData: Project full data to the sketch assay

In satijalab/seurat: Tools for Single Cell Genomics

Project full data to the sketch assay

Description

This function allows projection of high-dimensional single-cell RNA expression data from a full dataset onto the lower-dimensional embedding of the sketch of the dataset.

Usage

ProjectData(
  object,
  assay = "RNA",
  sketched.assay = "sketch",
  sketched.reduction,
  full.reduction,
  dims,
  normalization.method = c("LogNormalize", "SCT"),
  refdata = NULL,
  k.weight = 50,
  umap.model = NULL,
  recompute.neighbors = FALSE,
  recompute.weights = FALSE,
  verbose = TRUE
)

Arguments

object	A Seurat object.
assay	Assay name for the full data. Default is 'RNA'.
sketched.assay	Sketched assay name to project onto. Default is 'sketch'.
sketched.reduction	Dimensional reduction results of the sketched assay to project onto.
full.reduction	Dimensional reduction name for the projected full dataset.
dims	Dimensions to include in the projection.
normalization.method	Normalization method to use. Can be 'LogNormalize' or 'SCT'. Default is 'LogNormalize'.
refdata	An optional list for label transfer from sketch to full data. Default is NULL. Similar to refdata in 'MapQuery'
k.weight	Number of neighbors to consider when weighting labels for transfer. Default is 50.
umap.model	An optional pre-computed UMAP model. 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 the full data projected onto the sketched dimensional reduction results. The projected data are stored in the specified full reduction.

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.