ProjectIntegration: Integrate embeddings from the integrated sketched.assay
In satijalab/seurat: Tools for Single Cell Genomics

ProjectIntegration

R Documentation

Integrate embeddings from the integrated sketched.assay

Description

The main steps of this procedure are outlined below. For a more detailed description of the methodology, please see Hao, et al Biorxiv 2022: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2022.02.24.481684")}

Usage

ProjectIntegration(
  object,
  sketched.assay = "sketch",
  assay = "RNA",
  reduction = "integrated_dr",
  features = NULL,
  layers = "data",
  reduction.name = NULL,
  reduction.key = NULL,
  method = c("sketch", "data"),
  ratio = 0.8,
  sketched.layers = NULL,
  seed = 123,
  verbose = TRUE
)

Arguments

`object`	A Seurat object with all cells for one dataset
`sketched.assay`	Assay name for sketched-cell expression (default is 'sketch')
`assay`	Assay name for original expression (default is 'RNA')
`reduction`	Dimensional reduction name for batch-corrected embeddings in the sketched object (default is 'integrated_dr')
`features`	Features used for atomic sketch integration
`layers`	Names of layers for correction.
`reduction.name`	Name to save new reduction as; defaults to `paste0(reduction, '.orig')`
`reduction.key`	Key for new dimensional reduction; defaults to creating one from `reduction.name`
`method`	Methods to construct sketch-cell representation for all cells (default is 'sketch'). Can be one of: “`sketch`”: Use random sketched data slot “`data`”: Use data slot
`ratio`	Sketch ratio of data slot when `dictionary.method` is set to “`sketch`”; defaults to 0.8
`sketched.layers`	Names of sketched layers, defaults to all layers of “`object[[assay]]`”
`seed`	A positive integer. The seed for the random number generator, defaults to 123.
`verbose`	Print progress and message

Details

First learn a atom dictionary representation to reconstruct each cell. Then, using this dictionary representation, reconstruct the embeddings of each cell from the integrated atoms.