addPerCellQCMetrics: Add QC metrics to a SummarizedExperiment

In LTLA/scuttle: Single-Cell RNA-Seq Analysis Utilities

Add QC metrics to a SummarizedExperiment

Description

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

Usage

addPerCellQCMetrics(x, subsets = NULL, ..., subset.prefix = "subsets_")

addPerFeatureQCMetrics(x, ...)

addPerCellQC(x, subsets = NULL, ..., subset.prefix = "subsets_")

addPerFeatureQC(x, ...)

Arguments

x	A SummarizedExperiment object or one of its subclasses.
subsets	A named list containing one or more vectors (a character vector of feature names, a logical vector, or a numeric vector of indices), used to identify interesting feature subsets such as ERCC spike-in transcripts or mitochondrial genes.
...	For addPerCellQCMetrics, further arguments to pass to perCellQCMetrics. For addPerFeatureQCMetrics, further arguments to pass to perFeatureQCMetrics.
subset.prefix	String containing the prefix for the names of the columns of rowData that specify which genes belong to each subset. If NULL, these subset identity columns are not added to the rowData.

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 against duplicated column names.

addPerCellQC and addPerFeatureQC are exactly the same functions, sans the Metrics at the end of their names. They were added in the tempestuous youth of this package when naming was fast and loose. These can be considered to be soft-deprecated in favor of the longer forms.

Value

x is returned with the QC metrics added to the row or column metadata.

Author(s)

Aaron Lun, Lluís Revilla Sancho

See Also

perCellQCMetrics and perFeatureQCMetrics, which do the actual work.

Examples

example_sce <- mockSCE()
example_sce <- addPerCellQCMetrics(
     example_sce,
     subsets = list(group1 = 1:5, group2 = c("Gene_0001", "Gene_2000"))
)
colData(example_sce)
rowData(example_sce)

example_sce <- addPerFeatureQCMetrics(example_sce)
rowData(example_sce)

LTLA/scuttle documentation built on Oct. 28, 2024, 9:45 a.m.