isSpike: Get spike-in features in an SCESet object

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

Description

Get the features in the SCESet object that are spike-in controls, as specified using setSpike.

Usage

isSpike(object, ...)

## S4 method for signature 'SCESet'
isSpike(object, type = NULL, warning = TRUE)

Arguments

object	a SCESet object.
...	arguments passed through generic version of the function.
type	a character vector specifying the feature control sets to use. All specified spike-in sets in featureControlInfo(object) are used by default.
warning	A logical scalar specifying if a warning should be raised if spike-in controls are unavailable.

Value

A logical vector specifying if each row is a spike-in feature.

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"
summary(isSpike(example_sceset))

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