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SeuratObject (version 5.0.2)

split.StdAssay: Split an Assay

Description

Split an Assay

Usage

# S3 method for StdAssay
split(
  x,
  f,
  drop = FALSE,
  layers = c("counts", "data"),
  ret = c("assay", "multiassays", "layers"),
  ...
)
# S4 method for StdAssay
split(
  x,
  f,
  drop = FALSE,
  layers = c("counts", "data"),
  ret = c("assay", "multiassays", "layers"),
  ...
)

Value

Depends on the value of ret:

  • “assay”: x with the layers requested in layers split based on f; all other layers are left as-is

  • “multiassay”: a list of Assay5 objects; the list contains one value per split and each assay contains only the layers requested in layers with the key set to the split

  • “layers”: a list of matrices of length length(assays) * length(unique(f)); the list is named as “layer.split”

Arguments

x

An Assay5 object

f

a ‘factor’ in the sense that as.factor(f) defines the grouping, or a list of such factors in which case their interaction is used for the grouping. If x is a data frame, f can also be a formula of the form ~ g to split by the variable g, or more generally of the form ~ g1 + ... + gk to split by the interaction of the variables g1, ..., gk, where these variables are evaluated in the data frame x using the usual non-standard evaluation rules.

drop

logical indicating if levels that do not occur should be dropped (if f is a factor or a list).

layers

Names of layers to include in the split; pass NA for all layers; pass NULL for the default layer

ret

Type of return value; choose from:

  • “assay”: a single Assay5 object

  • “multiassay”: a list of Assay5 objects

  • “layers”: a list of layer matrices

...

Ignored

Progress Updates with <span class="pkg">progressr</span>

This function uses progressr to render status updates and progress bars. To enable progress updates, wrap the function call in with_progress or run handlers(global = TRUE) before running this function. For more details about progressr, please read vignette("progressr-intro")

See Also

v5 Standard Assay object, validity, and interaction methods $.StdAssay(), .DollarNames.StdAssay(), StdAssay-class, StdAssay-validity, [.StdAssay(), [[.StdAssay(), dim.StdAssay(), dimnames.StdAssay(), show,StdAssay-method, subset.StdAssay()