subsetPerSample: Subset Per Sample

In WeiSong-bio/roryk-bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description

Subset Per Sample

Usage

subsetPerSample(object, ...)

## S4 method for signature 'bcbioSingleCell'
subsetPerSample(object, minCells = 200L,
  assignAndSave = FALSE, envir = parent.frame(), dir = ".")

Arguments

object	Object.
...	Additional arguments.
minCells	Minimum number of cells required per sample.
assignAndSave	Assign and save the individual datasets.
envir	Environment where to assign the subsets. Only applicable when assignAndSave = TRUE.
dir	Output directory. Only applicable when assignAndSave = TRUE.

Value

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

• assignAndSave = TRUE: Subset file paths.

Author(s)

Michael Steinbaugh

See Also

Other Data Functions: aggregateReplicates, cell2sample, fetchGeneData, mapCellsToSamples, metricsPerSample, sampleData, selectSamples, topBarcodes

Examples

# bcbioSingleCell ====
# List mode (default)
list <- subsetPerSample(indrops_small, assignAndSave = FALSE)
names(list)

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

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

WeiSong-bio/roryk-bcbioSinglecell documentation built on July 6, 2019, 12:03 a.m.