calculateMetrics: Calculate quality control metrics

In acidgenomics/r-acidexperiment: Acid Genomics Summarized Experiment

Calculate quality control metrics

Description

Calculate quality control metrics

Usage

calculateMetrics(object, ...)

## S4 method for signature 'Matrix'
calculateMetrics(object, rowData = NULL, prefilter = FALSE)

## S4 method for signature 'SummarizedExperiment'
calculateMetrics(object, assay = 1L, prefilter = FALSE)

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

Arguments

object	Object.
rowData	DataFrame. Metadata describing the assay rows, if genomic ranges are not available. Use rowRanges (GenomicRanges) instead, if possible.
prefilter	logical(1). Drop very low quality samples/cells from the object. This can resize the number of columns but the rows (i.e. features) do not change with this operation.
assay	vector(1). Assay name or index position.
...	Additional arguments.

Details

Input a raw count matrix. Do not use size factor adjusted or log normalized counts here.

Value

• matrix / Matrix: DFrame containing metrics.

• SummarizedExperiment: Modified object, with metrics in colData().

Note

Updated 2021-09-11.

Author(s)

Michael Steinbaugh, Rory Kirchner

Examples

data(RangedSummarizedExperiment, package = "AcidTest")

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
names(SummarizedExperiment::colData(object))
object <- calculateMetrics(object)
names(SummarizedExperiment::colData(object))

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