calculateMetrics: Calculate quality control metrics

Description Usage Arguments Value Note Author(s) Examples

Description

Calculate quality control metrics

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
calculateMetrics(object, ...)

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

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

## S4 method for signature 'RangedSummarizedExperiment'
calculateMetrics(object, prefilter = FALSE)

## S4 method for signature 'SingleCellExperiment'
calculateMetrics(object, prefilter = FALSE)

Arguments

object

Object.

rowRanges

GRanges or GRangesList. Genomic ranges (e.g. genome annotations). Metadata describing the assay rows.

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.

...

Additional arguments.

Value

Note

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

Updated 2020-01-20.

Author(s)

Michael Steinbaugh, Rory Kirchner

Examples

1
2
3
4
5
6
data(SingleCellExperiment, package = "acidtest")

## SingleCellExperiment ====
object <- SingleCellExperiment
x <- calculateMetrics(object)
print(x)

acidgenomics/basejump documentation built on Aug. 15, 2020, 10:21 a.m.