topBarcodes: Top Barcodes

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

Description

Obtain the top cellular barcodes based on UMI counts.

Usage

topBarcodes(object, ...)

## S4 method for signature 'SingleCellExperiment'
topBarcodes(object, n = 1000L,
  return = c("data.frame", "list"))

## S4 method for signature 'seurat'
topBarcodes(object, n = 1000L, return = c("data.frame",
  "list"))

Arguments

object	Object.
...	Additional arguments.
n	Number of barcodes to return per sample.
return	Return type. Uses base::match.arg() internally and defaults to the first argument in the vector.

Value

• "list": list containing top barcodes as a character vector, split by sampleID.

• "data.frame": tibble grouped by sampleID and arranged by nUMI column in descending order. Cellular barcodes are in the cellID column.

Author(s)

Michael Steinbaugh

See Also

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

Examples

# SingleCellExperiment ====
# list
x <- topBarcodes(cellranger_small, return = "list")
lapply(x, class)

# data.frame
x <- topBarcodes(cellranger_small, return = "data.frame")
glimpse(x)

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