metrics: Quality control metrics

In acidgenomics/r-acidexperiment: Acid Genomics Summarized Experiment

Quality control metrics

Description

Quality control metrics

Usage

metrics(object, ...)

## S4 method for signature 'SummarizedExperiment'
metrics(object)

Arguments

object	Object.
...	Additional arguments.

Details

metrics() takes data stored in colData() and consistently returns a DFrame with sampleName and interestingGroups columns, even when these columns are not defined in colData(). This is designed to integrate with plotting functions that use ggplot2 internally.

Column names are always returned formatted in strict lower camel case.

This function will error intentionally if no numeric columns are defined in colData().

Value

DFrame.

Functions

• metrics(SummarizedExperiment): Sample-level metrics.

Note

Updated 2022-05-04.

Author(s)

Michael Steinbaugh, Rory Kirchner

Examples

data(RangedSummarizedExperiment, package = "AcidTest")

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
object <- calculateMetrics(object)
x <- metrics(object)
print(x)

acidgenomics/r-acidexperiment documentation built on Jan. 17, 2024, 7:56 p.m.