subsetPerSample: Subset per sample

In acidgenomics/r-acidsinglecell: Acid Genomics Single Cell Experiment

Subset per sample

Description

Subset per sample

Usage

subsetPerSample(object, ...)

## S4 method for signature '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)
names(list)

## Assign and save mode (useful for large datasets).
subsetPerSample(
    object = object,
    assignAndSave = TRUE,
    envir = parent.frame(),
    dir = "subsetPerSample"
)
sort(list.files("subsetPerSample"))

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

acidgenomics/r-acidsinglecell documentation built on March 30, 2024, 5:39 a.m.