addPerCellQC {scater}R Documentation

Add QC to an SE

Description

Convenient utilities to compute QC metrics and add them to a SummarizedExperiment's metadata.

Usage

addPerCellQC(x, ...)

addPerFeatureQC(x, ...)

Arguments

x

A SummarizedExperiment object or one of its subclasses.

...

For addPerCellQC, further arguments to pass to perCellQCMetrics.

For addPerFeatureQC, further arguments to pass to perFeatureQCMetrics.

Details

These functions are simply wrappers around perCellQCMetrics and perFeatureQCMetrics, respectively. The computed QC metrics are automatically appended onto the existing colData or rowData. No protection is provided to avoid duplicated column names.

Value

An object like x but with the QC metrics added to the row or column metadata.

Author(s)

Aaron Lun

See Also

perCellQCMetrics and perFeatureQCMetrics, which do the actual work.

Examples

example_sce <- mockSCE()
example_sce <- addPerCellQC(example_sce)
colData(example_sce)

example_sce <- addPerFeatureQC(example_sce)
rowData(example_sce)
[Package scater version 1.16.2 Index]