as_SingleCellExperiment: Coerce an object into a 'SingleCellExperiment'
In keyes-timothy/tidytof: Analyze High-dimensional Cytometry Data Using Tidy Data Principles

as_SingleCellExperiment

R Documentation

Coerce an object into a `SingleCellExperiment`

Description

Coerce an object into a SingleCellExperiment

Coerce a tof_tbl into a SingleCellExperiment

Usage

as_SingleCellExperiment(x, ...)

## S3 method for class 'tof_tbl'
as_SingleCellExperiment(
  x,
  channel_cols = where(tof_is_numeric),
  reduced_dimensions_cols,
  metadata_cols = where(function(.x) !tof_is_numeric(.x)),
  split_reduced_dimensions = FALSE,
  ...
)

Arguments

`x`	A tof_tbl
`...`	Unused.
`channel_cols`	Unquoted column names representing columns that contain single-cell protein measurements. Supports tidyselect helpers. If nothing is specified, the default is all numeric columns.
`reduced_dimensions_cols`	Unquoted column names representing columns that contain dimensionality reduction embeddings, such as tSNE or UMAP embeddings. Supports tidyselect helpers.
`metadata_cols`	Unquoted column names representing columns that contain metadata about the samples from which each cell was collected. If nothing is specified, the default is all non-numeric columns.
`split_reduced_dimensions`	A boolean value indicating whether the dimensionality results in x should be split into separate slots in the resulting `SingleCellExperiment`. If FALSE (the default), the split will not be performed and the `reducedDims` slot in the result will have a single entry ("tidytof_reduced_dimensions"). If TRUE, the split will be performed and the `reducedDims` slot in the result will have 1-4 entries depending on which dimensionality reduction results are present in x ("tidytof_pca", "tidytof_tsne", "tidytof_umap", and "tidytof_reduced_dimensions"). Note that "tidytof_reduced_dimensions" will include all dimensionality reduction results that are not named according to tidytof's pca, umap, and tsne conventions.