metrics: Sample Barcode Metrics

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

Description

Sample Barcode Metrics

Usage

## S4 method for signature 'matrix'
metrics(object, rowData = NULL, prefilter = FALSE)

## S4 method for signature 'dgCMatrix'
metrics(object, rowData = NULL, prefilter = FALSE)

## S4 method for signature 'dgTMatrix'
metrics(object, rowData = NULL, prefilter = FALSE)

## S4 method for signature 'SingleCellExperiment'
metrics(object, interestingGroups)

## S4 method for signature 'seurat'
metrics(object, ...)

Arguments

object	Object.
rowData	Data describing the rows of the object.
prefilter	Whether to apply pre-filtering to the cellular barcodes.
interestingGroups	Character vector of interesting groups. Must be formatted in camel case and intersect with sampleData() colnames.
...	Additional arguments.

Value

data.frame with cellular barcodes as rows.

Author(s)

Michael Steinbaugh, Rory Kirchner

See Also

Other Quality Control Functions: barcodeRanksPerSample, filterCells, plotCellCounts, plotGenesPerCell, plotMitoRatio, plotMitoVsCoding, plotNovelty, plotQC, plotReadsPerCell, plotUMIsPerCell, plotZerosVsDepth

Examples

# SingleCellExperiment ====
x <- metrics(cellranger_small)
glimpse(x)

# dgCMatrix ====
counts <- counts(cellranger_small)
class(counts)
x <- metrics(counts)
glimpse(x)

roryk/bcbioSinglecell documentation built on May 27, 2019, 10:44 p.m.