splitAltExps: Split off alternative features
In SingleCellExperiment: S4 Classes for Single Cell Data

Description Usage Arguments Details Value Author(s) See Also Examples

Split a SingleCellExperiment based on the feature type, creating alternative Experiments to hold features that are not in the majority set.

1	splitAltExps(x, f, ref = NULL)

`x`	A SingleCellExperiment object.
`f`	A character vector or factor of length equal to `nrow(x)`, specifying the feature type of each row.
`ref`	String indicating which level of `f` should be treated as the main set.

This function provides a convenient way to create a SingleCellExperiment with alternative Experiments. For example, a SingleCellExperiment with rows corresponding to all features can be quickly split into endogenous genes (main) and other alternative features like spike-in transcripts and antibody tags.

By default, the most frequent level of f is treated as the ref if the latter is not specified.

A SingleCellExperiment where each row corresponds to a feature in the main set. Each other feature type is stored as an alternative Experiment, accessible by altExp.

Aaron Lun

altExp, to access and manipulate the alternative Experiment fields.

example(SingleCellExperiment, echo=FALSE)
feat.type <- sample(c("endog", "ERCC", "CITE"), nrow(sce),
    replace=TRUE, p=c(0.8, 0.1, 0.1))

sce2 <- splitAltExps(sce, feat.type)
sce2

Loading required package: SummarizedExperiment
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    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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Loading required package: IRanges
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Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

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class: SingleCellExperiment 
dim: 164 100 
metadata(0):
assays(2): counts logcounts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):
reducedDimNames(2): PCA tSNE
altExpNames(2): CITE ERCC