Subset per sample

Subset per sample

Usage

subsetPerSample(object, ...)

# S4 method for class 'SingleCellExperiment'
subsetPerSample(
  object,
  minCells = 1L,
  assignAndSave = FALSE,
  envir = parent.frame(),
  dir = getwd()
)

Arguments

object

Object.

minCells

integer(1). Minimum number of cells required per sample.

assignAndSave

logical(1). Assign and save the individual datasets.

envir

environment. Where to assign the subsets. Only applicable when assignAndSave = TRUE.

dir

character(1). Output directory. Only applicable when assignAndSave = TRUE.

...

Additional arguments.

Value

• assignAndSave = FALSE: Per sample objects in a list.

• assignAndSave = TRUE: Subset file paths.

Note

Updated 2022-03-02.

Examples

data(SingleCellExperiment_splatter, package = "AcidTest")

## SingleCellExperiment ====
object <- SingleCellExperiment_splatter

## List mode (default).
list <- subsetPerSample(object, assignAndSave = FALSE)
#> Error in vapply(X = X, FUN = FUN, FUN.VALUE = logical(1L), ..., USE.NAMES = useNames): formal argument "USE.NAMES" matched by multiple actual arguments
names(list)
#> NULL

## Assign and save mode (useful for large datasets).
subsetPerSample(
    object = object,
    assignAndSave = TRUE,
    envir = parent.frame(),
    dir = "subsetPerSample"
)
#> Error in vapply(X = X, FUN = FUN, FUN.VALUE = logical(1L), ..., USE.NAMES = useNames): formal argument "USE.NAMES" matched by multiple actual arguments
sort(list.files("subsetPerSample"))
#> character(0)

## Clean up.
unlink("subsetPerSample", recursive = TRUE)