spikes: Extract expression values for spike-in features in an SCESet...

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

Description

Extract a matrix of expression values for features in spike-in control sets.

Usage

spikes(object, ...)

## S4 method for signature 'SCESet'
spikes(object, exprs_values = "counts", type = NULL)

Arguments

object	a SCESet object.
...	arguments passed through generic version of the function.
exprs_values	a string specifying the type of expression values to extract.
type	a character vector containing the names of the spike-in control sets to extract. By default, expression values for features in all spike-in control sets are extracted.

Details

If exprs_values="exprs", users should have run normalize(object) first, so that spike-in features are normalized with spike-in size factors.

Value

A matrix of expression values for features in the specified spike-in control sets.

Author(s)

Aaron Lun

Examples

data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data = sc_example_cell_info)
example_sceset <- newSCESet(countData = sc_example_counts, phenoData = pd)
example_sceset <- calculateQCMetrics(example_sceset,
                            feature_controls = list(ERCC = 1:40, Mito=41:50))
setSpike(example_sceset) <- "ERCC"
head(spikes(example_sceset))

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.