Gets or sets the rows corresponding to spike-in transcripts.
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## S4 method for signature 'SingleCellExperiment,character' isSpike(x, type) ## S4 method for signature 'SingleCellExperiment,missing' isSpike(x, type) ## S4 method for signature 'SingleCellExperiment,NULL' isSpike(x, type) ## S4 replacement method for signature 'SingleCellExperiment,character' isSpike(x, type) <- value ## S4 method for signature 'SingleCellExperiment' spikeNames(x)
A SingleCellExperiment object.
A string containing the name of the spike-in set.
A vector indicating which rows correspond to spike-in transcripts.
Spike-in transcripts may be added during library preparation in single-cell RNA sequencing experiments. These usually need to be handled differently during data analysis, compared to the endogenous genes. Thus, it is important to indicate which rows correspond to spike-in transcripts.
isSpike<- method accepts any
value that indicates which rows correspond to spike-ins.
This can be a logical or integer subsetting vector, or a vector of row names.
type should be set to the name of the spike-in set, e.g.,
In this manner, multiple types of spike-in sets are supported for a single experiment.
The names of all available spike-in sets can be obtained using
To remove spike-ins for a particular set,
value should be set to
NULL when using
isSpike getter methods will return a logical vector indicatng which rows represent spike-ins of the set specified by
type is missing or
NULL, the vector will instead indicate whether each row is in any spike-in set.
type is specified but not available, an error will be raised.
isSpike, a logical vector is returned indicating whether each row is in the specified set
type or any set.
isSpike<-, a SingleCellExperiment is returned with spike-in information stored in the internal metadata fields.
spikeNames, a character vector is returned containing the names of available spike-in sets.
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