ProjectCellEmbeddings: Project query data to the reference dimensional reduction
In satijalab/seurat: Tools for Single Cell Genomics

ProjectCellEmbeddings

R Documentation

Project query data to the reference dimensional reduction

Description

Project query data to the reference dimensional reduction

Usage

ProjectCellEmbeddings(query, ...)

## S3 method for class 'Seurat'
ProjectCellEmbeddings(
  query,
  reference,
  query.assay = NULL,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  normalization.method = c("LogNormalize", "SCT"),
  scale = TRUE,
  verbose = TRUE,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

## S3 method for class 'Assay'
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

## S3 method for class 'SCTAssay'
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

## S3 method for class 'StdAssay'
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

## Default S3 method:
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  features = NULL,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  ...
)

## S3 method for class 'IterableMatrix'
ProjectCellEmbeddings(
  query,
  reference,
  reference.assay = NULL,
  reduction = "pca",
  dims = 1:50,
  scale = TRUE,
  normalization.method = NULL,
  verbose = TRUE,
  features = features,
  nCount_UMI = NULL,
  feature.mean = NULL,
  feature.sd = NULL,
  block.size = 10000,
  ...
)

Arguments

`query`	An object for query cells
`reference`	An object for reference cells
`query.assay`	Assay name for query object
`reference.assay`	Assay name for reference object
`reduction`	Name of dimensional reduction from reference object
`dims`	Dimensions used for reference dimensional reduction
`scale`	Determine if scale query data based on reference data variance
`verbose`	Print progress
`feature.mean`	Mean of features in reference
`feature.sd`	Standard variance of features in reference